Re: [gmx-users] protein near the edges of simulation box

Oh, Thanks a lot. That is really  kind of you.   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 9:13 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 6/15/12 12:41 PM

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:41 PM, Shima Arasteh wrote: Thanks. Sorry, what do you mean by trajectory A and B? It's just a generic example. To be absolutely clear, let's say you have a trajectory named "md.xtc" that mdrun produces. That trajectory will have molecules that diffuse all over the place. Y

Re: [gmx-users] protein near the edges of simulation box

Thanks. Sorry, what do you mean by trajectory A and B?   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 9:04 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 6/15/12 12:19

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:19 PM, Shima Arasteh wrote: OK, but as I know the trjconv is a command after mdrun, so when I get the output of mdrun and see it in VMD, it doesn't make different. Now wondering what is the benefit of trjconv -center and -pbc? You have to load the output trajectory from trjc

Re: [gmx-users] protein near the edges of simulation box

Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, June 15, 2012 8:24 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 6/15/12 11:46 AM, Shima Arasteh wrote: > Dear Elton, > Where am I supposed to use trjconv -center ? when I want to get the mdrun? trjcon

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 5:46 PM, Shima Arasteh wrote: > Dear Elton, > Where am I supposed to use trjconv -center ? when I want to get the mdrun? > As Justin mentioned, you should use if after mdrun, on your .xtc (or.trr) files. Check the manual. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dep

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 11:46 AM, Shima Arasteh wrote: Dear Elton, Where am I supposed to use trjconv -center ? when I want to get the mdrun? trjconv is a post-processing command that can be used for a variety of purposes, of which one of the more common ones is to transform coordinates for convenient v

Re: [gmx-users] protein near the edges of simulation box

Dear Elton, Where am I supposed to use trjconv -center ? when I want to get the mdrun?   Sincerely, Shima From: Elton Carvalho To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:43 PM Subject: Re: [gmx-users] protein near the edges of

Re: [gmx-users] protein near the edges of simulation box

Thanks.   Sincerely, Shima From: Elton Carvalho To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:43 PM Subject: Re: [gmx-users] protein near the edges of simulation box On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar wrote: > You

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar wrote: > You can specify the protein to have no net center of mass > motion, by setting it as comm_grps in the .mdp file. > If the user is just concerned about visualization, trjconv -center solves his problem. -- Elton Carvalho Tel.: +55 11 309

Re: [gmx-users] protein near the edges of simulation box

otein? > Is it possible for box to be defined every step?, then the protein would > stay in the center of the box. > > Sincerely, > Shima > > From: Mark Abraham > To: Discussion list for GROMACS users > Sent: Thursday, June 14, 2012 12:22

Re: [gmx-users] protein near the edges of simulation box

incerely, > Shima > From: Mark Abraham > To: Discussion list for GROMACS users > Sent: Thursday, June 14, 2012 12:22 PM > Subject: Re: [gmx-users] protein near the edges of simulation box > > On 14/06/2012 5:47 PM, Shima Arasteh wrote: >> >> Dear gmx friends, >

Re: [gmx-users] protein near the edges of simulation box

y, June 14, 2012 12:22 PM *Subject:* Re: [gmx-users] protein near the edges of simulation box On 14/06/2012 5:47 PM, Shima Arasteh wrote: Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near on

Re: [gmx-users] protein near the edges of simulation box

.   Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Thursday, June 14, 2012 12:22 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 14/06/2012 5:47 PM, Shima Arasteh wrote: Dear gmx friends, > >

Re: [gmx-users] Protein near the edges of simulation box

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, Tsjerk On Thu, Jun 14, 2012 at 10:26 AM, Shima Arasteh wrote: > > Dear gmx friends, > > I put a protein in a simulation box filled of water molecules and entered > the mdrun command. After the simulation, I fo

[gmx-users] Protein near the edges of simulation box

Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? Does it mean that the simulation is meaning

Re: [gmx-users] protein near the edges of simulation box

On 14/06/2012 5:47 PM, Shima Arasteh wrote: Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me?

[gmx-users] protein near the edges of simulation box

Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? Does it mean that the simulation is meaningles