Re: [gmx-users] output file format under pbc

Dear Gromacs Users, I would like to describe the situation. An initial molecule in the periodic boundary condition is located near the right side of box. The box is big, thus needs to be adjusted and equilibrated under NPT. The box should be shrinked after few ns seconds. The molecule near the

Re: [gmx-users] output file format under pbc

You can use VMD to visually wrap the molecules by typing: pbc wrap -compound res -all In the command interface on VMD. -Evan L. On Aug 25, 2016 8:06 PM, "Chang Woon Jang" wrote: > Dear Sir, > >Attached are figures here. > > Thank you. > > Best regards, >

Re: [gmx-users] output file format under pbc

On 8/25/16 10:06 PM, Chang Woon Jang wrote: Dear Sir, Attached are figures here. The mailing list does not accept attachments. Follow the previous link about PBC and consult Google. Using trjconv comes up daily on this mailing list. -Justin --

Re: [gmx-users] output file format under pbc

Dear Sir, Attached are figures here. Thank you. Best regards, Changwoon Jang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] output file format under pbc

Hi, I can't find your figures and I guess this link may be helpful to you: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions On 26 August 2016 at 09:49, Chang Woon Jang wrote: > Dear Gromacs Users, > > Sorry for the misspelling of

Re: [gmx-users] output file format under pbc

Dear Gromacs Users, Sorry for the misspelling of "Grimaces Users" due to automatic predictive text function. I am waiting for the answer. Thank you. Best regards, Changwoon Jang -- Gromacs Users mailing list * Please search the archive at

[gmx-users] output file format under pbc

Dear Grimaces Users, When I run a simulation with NPT under periodic boundary condition, the output file (confout.gro) is obtained with shrinked box due to the external pressure. Because of the periodic boundary condition, some molecules might be cross the boundary appearing the other side of

Re: [gmx-users] LINCS warning

On 8/25/16 5:56 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello users, I was trying to energy minimize my system of protein embedded in bilayer. But I am receiving the following error: Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max

[gmx-users] LINCS warning

Hello users, I was trying to energy minimize my system of protein embedded in bilayer. But I am receiving the following error: Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max 0.149038 (between atoms 21616 and 21619) bonds that rotated more