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

farzaneh sarrami sarrami... at gmail.com
Wed Oct 16 08:06:01 UTC 2019

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

On Tue, Oct 8, 2019 at 5:22 PM Travis <polla... at gmail.com> 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.
>>> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/4b2a5d18-4e0d-43e4-8bd8-e2c906f92cfe%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/4b2a5d18-4e0d-43e4-8bd8-e2c906f92cfe%40googlegroups.com?utm_medium=email&utm_source=footer>
> .

*Farzaneh Sarrami*
Post-doctoral Fellow

Laboratory of Organic Electronic
Linköping University
Create your own email signature
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191016/f9e627a6/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PEDOT-36-10000-6-31+G-try32.inp
Type: application/octet-stream
Size: 2053 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191016/f9e627a6/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PEDOT-O2-35H2O-H3O+-try32-pos-1.xyz
Type: chemical/x-xyz
Size: 2169795 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191016/f9e627a6/attachment.xyz>

More information about the CP2K-user mailing list