[gmx-users] Some molecules disconnected into many parts after EM
ysong30 at asu.edu
Fri May 8 19:53:44 CEST 2009
Thanks for your message.
When I open the gro file using VMD it shows:
I was thinking the problem may not come from the artifact of visualization.
Since if the gro file is fine it should be like:
because I have 6 chains in the box.
This morning I found that it seems the problem was resolved by increasing
the box size. Why is that?
On Thu, May 7, 2009 at 5:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Yanmei Song wrote:
>> Dear users:
>> I set up a 8nm cubic box with 6 long chain molecules. After EM, there is
>> no error message. However I found that in the gro file by visualization, 2
>> of the chains has been split in many parts, which means many bonds in the
>> molecules disconnected. And also the other 4 are good. I checked em.log and
>> eveyting looks fine.
>> Steepest Descents converged to machine precision in 1545 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy = -7.51461594735782e+03
>> Maximum force = 2.66505909651672e+02 on atom 1256
>> Norm of force = 9.84300153087768e+00
>> Anyone knows how to solve the problem? Thanks in advance!
> Probably an artifact of visualization, or otherwise periodic boundary
>> Yanmei Song
>> Department of Chemical Engineering
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Department of Chemical Engineering
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users