[CP2K-user] [CP2K:12324] Re: Molecules moving out of simulation cell in AIMD simulation

Travis polla... at gmail.com
Thu Oct 17 18:48:51 UTC 2019


CP2K prints the unwrapped coordinates. Molecules diffusing out of the box 
are not wrapped back in. You can view the wrapped trajectory in VMD by 
opening the TK console,

pbc set {15 15 20} -all
pbc box
pbc wrap -all

If you're trying to perform a bulk calculation, you will need to remove the 
vacuum region either by CELL_OPT with fixed angles or by filling the void 
spaces with water.


On Wednesday, October 16, 2019 at 5:06:25 AM UTC-3, farzaneh sarrami wrote:
> Hi Travis,
> Thanks for complete explanation. Currently I am using NVE for MD part in 
> my system. I tried to use NPT but it doesn't work for my system. So I 
> prefer to stick to NVE as it goes to the right direction. I am still 
> struggling with water molecules moving out of the simulation box. I have 
> enclosed my input file and final coordinates.
> Would you please have a look and give me some advises to fix this problem?
> Many thanks in advance
> Farzaneh
> On Tue, Oct 8, 2019 at 5:22 PM Travis <po... at gmail.com <javascript:>> 
> wrote:
>> Hi,
>> Compile the code with your preferred Fortran compiler,
>> gfortran dumpdcd.f90
>> Run code on a host of DCD files you want to merge, these would be coming 
>> from a long simulation that you broke up into smaller segments,
>> ./a.out -xyz reference.xyz -pbc -of dcd -o full_foo_trajectory.dcd foo1.dcd 
>> foo2.dcd foo3.dcd ... fooN.dcd
>> You need a reference XYZ format file for determining atom name as DCD 
>> only contains lattice parameters and coordinates. The -pbc flag says to 
>> produce a wrapped trajectory, while leaving it off produces the unwrapped 
>> trajectory.
>> To wrap an XYZ trajectory requires TRAVIS (
>> https://www.travis-analyzer.de/). In one of the advanced options, you 
>> can read the second line for each frame of the XYZ file as the lattice 
>> parameters in Angstroms and degrees. I give a more detailed explanation of 
>> it here, https://groups.google.com/forum/#!topic/cp2k/GNLdTcUZFUo (for 
>> NPT). Alternatively, if you are comfortable with Python, you can use the 
>> Atomic Simulation Environment.
>> -T
>> On Tuesday, October 8, 2019 at 4:23:27 AM UTC-3, farzaneh sarrami wrote:
>>> Thanks Travis,
>>> Would you please explain in more details how can I use dumpdcd.f90 
>>> script in cp2k ? as I have same problem.
>>> Best,
>>> Farzaneh
>>> On Monday, October 7, 2019 at 5:01:01 PM UTC+2, Travis wrote:
>>>> Hi,
>>>> CP2K dumps unwrapped coordinates, so they are not imaged back into the 
>>>> box if they drift beyond. A simple way to get a wrapped trajectory is to 
>>>> dump DCD files during MD, then use the dumpdcd.f90 script in tools/ to dump 
>>>> a wrapped DCD (-pbc option). I don't recommend writing XYZ format 
>>>> trajectories for MD. Write DCD and convert. Way easier to strip info than 
>>>> to add it back in.
>>>> -T
>>>> On Monday, October 7, 2019 at 8:09:09 AM UTC-3, Harender Singh wrote:
>>>>> Dear all, 
>>>>> I am running AIMD simulation of some electrolyte at Li electrode. 
>>>>> While the electrolyte molecules are staying within the simulation cell, the 
>>>>> electrode atoms are moving out of the cell. 
>>>>> Is there any possible explanation for that?
>>>>> Is there something wrong with my simulation setup? If yes, then how 
>>>>> can I correct it?
>>>>> Thanks for the help in advance. 
>>>> -- 
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>> .
> -- 
> *Farzaneh Sarrami*
> Post-doctoral Fellow 
> Laboratory of Organic Electronic 
> Linköping University 
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