Dear Pablo<br>The input files are in the tar archive. <br>Actually, I found a post in this list about a similar problem with AMBER prmtop files.<br>Then I tried to put the number (456) of the molecule analysing the output of the MOLECULE print_key (it is the .mol file in the tar archive).<br>
However the message is that the constrainted atoms are not in the 456 molecule.<br>Maybe I'm reading the molecule number in a wrong place.<br><br><br>Thanks again<br><br>Jacopo<br><div class="gmail_quote">2011/10/17 Campomanes Ramos Pablo <span dir="ltr"><<a href="mailto:pablo.ca...@epfl.ch">pablo.ca...@epfl.ch</a>></span><br>
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt;">Dear Jacopo,<br>
<br>
I think that the message is clear. The code cannot find the MOLNAME defined for constraints, and therefore I assume that constraints are not applied. However, it is difficult to guess where your problem is (pdb, topology file...) without having a look at your
input(s) file(s)... Could you please post them here?<br>
<br>
Regards,<br>
Pablo.<br>
<br>
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<div style="direction: ltr;"><font color="#000000" face="Tahoma" size="2"><div class="im"><b>From:</b> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> [<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>] on behalf of Jacopo Sgrignani [<a href="mailto:sgr...@gmail.com" target="_blank">sgr...@gmail.com</a>]<br>
</div><b>Sent:</b> Monday, October 17, 2011 1:44 PM<br>
<b>To:</b> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><br>
<b>Subject:</b> Re: [CP2K:3530] restraint dihedral<br>
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<div>Thanks Pablo for your suggestion, I'm trying this solution.<br>
However I have a problem with the keyword MOLNAME or <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#list_MOLECULE" target="_blank">
MOLECULE</a>, actually<br>
I tried both the keyword MOLECULE with the resid number from the PDB input file, and<br>
the keyword MOLNAME with the resname fromthe pdb, but they don't seem to be the right solutions.<br>
Actually using MOLECULE with the resname the simulation start but in the output I find this warning:<br>
<br>
<br>
*** 13:22:30 WARNING in topology_constraint_util:print_warning_molname ***<br>
*** MOLNAME (ASD) was defined for constraints, but this molecule ***<br>
*** name is not defined. Please check carefully your PDB, PSF (has ***<br>
*** priority over PDB) or input driven CP2K coordinates. In case you may ***<br>
*** not find the reason for this warning it may be a good idea to print ***<br>
*** all molecule information (including kind name) activating the ***<br>
*** print_key MOLECULES specific of the SUBSYS%PRINT section.<br>
Then I used also the MOLECULES print_key but the number of the molecule where the constrainted atoms are, it is
<br>
the same of the resid number in the PDB.<br>
<br>
Can somebody help me? Is it this waring important or the costraint is applied?<br>
<br>
<div class="gmail_quote">Thanks again<br>
<br>
Jacopo<br>
<br>
2011/10/16 Campomanes Ramos Pablo <span dir="ltr"><<a href="mailto:pablo.ca...@epfl.ch" target="_blank">pablo.ca...@epfl.ch</a>></span><br>
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Dear Jacopo,<br>
<br>
I think you can easily solve your problem if you have a look at:<br>
<br>
<a href="http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE/RESTRAINT.html" target="_blank">http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE/RESTRAINT.html</a><br>
<br>
Best regards,<br>
Pablo.<br>
<br>
-----------------------------------------------<br>
<b style="font-weight: normal;">Pablo Campomanes </b>
<p><br>
Tel:<a href="tel:%2B%2B41-%280%2921-693-0326" value="+41216930326" target="_blank">++41-(0)21-693-0326</a>
<br>
Fax: <a href="tel:%2B%2B41-%280%2921-693-0320" value="+41216930320" target="_blank">
++41-(0)21-693-0320</a> <br>
Email: <a href="mailto:pablo.ca...@epfl.ch" target="_blank">pablo.ca...@epfl.ch</a></p>
<p><br>
</p>
<p>Laboratory of Computational<br>
Chemistry and Biochemistry <br>
BCH 4118 EPF Lausanne<br>
CH-1015 Lausanne </p>
------------------------------------------------<br>
<br>
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<div style="direction: ltr;"><font color="#000000" face="Tahoma" size="2"><b>From:</b>
<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> [<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>] on behalf of Jacopo Sgrignani [<a href="mailto:sgr...@gmail.com" target="_blank">sgr...@gmail.com</a>]<br>
<b>Sent:</b> Sunday, October 16, 2011 4:09 PM<br>
<b>To:</b> <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a><br>
<b>Subject:</b> [CP2K:3528] restraint dihedral<br>
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<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">Dear All</span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">I would like to know the best way to restrict a dihedral angle during a simulation.</span><span style="font-size: 10pt; font-family: Times;" lang="EN-GB"></span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">Without any experience about this, I tried to use a fictitious Colvar putting two walls to define the space that the dihedral can freely explore. Then, the program asks for a
value of the SCALE variable during the metadynamics calculation, and I set this to 0.</span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">However, I'm not sure that this is the correct solution to my problem.</span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">Can somebody suggest me other solutions?</span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">Thanks</span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-family: Arial; color: black;" lang="EN-GB">Jacopo</span></p>
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