Re: [gmx-users] trjconv and -pbc

2011-10-28 Thread Tsjerk Wassenaar
Hi Lina, You first remove the jumps from the trajectory. Then you can view that trajectory with ngmx or with VMD. You can also then extract the frames around the 'jump' and look at them. But if the molecule goes unstuck and then crosses the boundary to get stuck to the protein again, it would give

Re: [gmx-users] trjconv and -pbc

2011-10-28 Thread lina
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > My previous reply was from before I looked at the graph. Have you > considered that the molecule might be taking a stroll and turn back, Ha ... stroll?! > or goes to another side of the protein? Have you looked at the > trajec

Re: [gmx-users] trjconv and -pbc

2011-10-28 Thread Tsjerk Wassenaar
Hi Lina, My previous reply was from before I looked at the graph. Have you considered that the molecule might be taking a stroll and turn back, or goes to another side of the protein? Have you looked at the trajectory, in particular at the trajectory with the jumps removed? Cheers, Tsjerk On Fr

Re: [gmx-users] trjconv and -pbc

2011-10-28 Thread Tsjerk Wassenaar
Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work. Cheers, Tsjerk On Oct 28, 2011 9:01 AM, "lina" wr

Re: [gmx-users] trjconv and -pbc

2011-10-28 Thread lina
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidis

Re: RE: [gmx-users] trjconv and -pbc

2011-10-27 Thread Tsjerk Wassenaar
Vijaya, Can you explain how you think that may help solve the problem? I think it won't. Tsjerk On Oct 28, 2011 7:40 AM, "vijaya subramanian" wrote: -pbc atom -- Date: Fri, 28 Oct 2011 06:34:28 +0200 Subject: Re: [gmx-users] trjconv and

RE: [gmx-users] trjconv and -pbc

2011-10-27 Thread vijaya subramanian
-pbc atom Date: Fri, 28 Oct 2011 06:34:28 +0200 Subject: Re: [gmx-users] trjconv and -pbc From: tsje...@gmail.com To: gmx-users@gromacs.org Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Tsjerk On Oct 28, 2011 6:27 AM, "lina" wrot

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread Tsjerk Wassenaar
Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, Tsjerk On Oct 28, 2011 6:27 AM, "lina" wrote: On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Make su... I used the initial mdrun .tpr. After checking the generated p

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread lina
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar wrote: > Hi Lina, > > Make sure to use a reference in which the molecules are together (clustered) > the way you want them. I used the initial mdrun .tpr. After checking the generated pdb (total 51 frames), the first 28/29 frames both are togethe

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread lina
[gmx-users-boun...@gromacs.org] on >>> behalf of lina [lina.lastn...@gmail.com] >>> Sent: Thursday, October 27, 2011 10:47 AM >>> To: Discussion list for GROMACS users >>> Subject: [gmx-users] trjconv and -pbc >>> >>> Hi, >>> >>> I

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread Tsjerk Wassenaar
Hi Lina, Make sure to use a reference in which the molecules are together (clustered) the way you want them. Cheers, Tsjerk On Oct 27, 2011 11:47 AM, "lina" wrote: Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread Mark Abraham
: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together

Re: [gmx-users] trjconv and -pbc

2011-10-27 Thread lina
n list for GROMACS users > Subject: [gmx-users] trjconv and -pbc > > Hi, > > I have a problem using > > trjconv_g -pbc nojump > or > > trjconv_g -pbc nojump -center > > I even tried the -pbc whole. > > The system is protein with a small molecular, for the first

RE: [gmx-users] trjconv and -pbc

2011-10-27 Thread Marzinek, Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of lina [lina.lastn...@gmail.com] Sent: Thursday, October 27, 2011 10:47 AM To: Discussion list for GROMACS users Subject: [gmx-users] trjconv and -pbc Hi, I have a problem

[gmx-users] trjconv and -pbc

2011-10-27 Thread lina
Hi, I have a problem using trjconv_g -pbc nojump or trjconv_g -pbc nojump -center I even tried the -pbc whole. The system is protein with a small molecular, for the first time period, when I checked on pymol. they are together, but later they apart, after show cell, protein inside the cell, wh