Re: [gmx-users] trjconv problem for two groups

Liu Shiyong wrote: Dear all, I tried to output protein-ligand complex from trr file . Could I select both Group 2 and Group 12 at the same time ? Or I have to run this command for every group , respectively? Use make_ndx to merge the groups and pass the index file to trjconv. -Justin

[gmx-users] trjconv problem for two groups

Dear all, I tried to output protein-ligand complex from trr file . Could I select both Group 2 and Group 12 at the same time ? Or I have to run this command for every group , respectively? Select group for output Opening library file /usr/share/gromacs/top//aminoacids.dat Group 0 (

Re: [gmx-users] trjconv problem

...@vt.edu; Discussion list for GROMACS users *Sent:* Thu, May 5, 2011 10:33:19 AM *Subject:* Re: [gmx-users] trjconv problem Hi Justin, In many of the frames, if I use -b and -e to be same , it works For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 16ps. But, in

Re: [gmx-users] trjconv problem

I found it will work if I use -b 13.9 -e 14.1 From: Sanku M To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Thu, May 5, 2011 10:33:19 AM Subject: Re: [gmx-users] trjconv problem Hi Justin, In many of the frames, if I use -b and -e to be same

Re: [gmx-users] trjconv problem

utput, trajectory ended at 14' Any help will be appreciated. Sanku From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thu, May 5, 2011 10:22:38 AM Subject: Re: [gmx-users] trjconv problem Sanku M wrote: > Hi, > I am having a problem wit

Re: [gmx-users] trjconv problem

Sanku M wrote: Hi, I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 . If I try to get a snapshot corresponding to 14 ps, I was trying to use "-b 14 -e 14 " command as follows. But, If I issue this command as shown below trjconv

[gmx-users] trjconv problem

Hi, I am having a problem with trjconv to get a single snap-shot from a trajectory file. I am using gromacs 4.0.7 . If I try to get a snapshot corresponding to 14 ps, I was trying to use "-b 14 -e 14 " command as follows. But, If I issue this command as shown below trjconv --f traj.xtc -o c

Re: [gmx-users] trjconv problem

Hi Алексей, We have no use for your PDB files anyway :) In order not to loose the phospho from your tyrosine, you want to start out with trjconv -pbc whole. To obtain what you desire, you probably want to give the following a good read: http://www.gromacs.org/Documentation/Terminology/Periodic_Bou

[gmx-users] trjconv problem

Hi, I want to ask you for help. I've got a trr file after 5 ns simulation on the desktop 2 quad. The object is a complex of protein and ligand (the itp file for ligand was prepeared by server), in adition, I made some changes in rtp, atp, bon.itp databases to obtain a phosphorylated tyrosine. When

RE: [gmx-users] trjconv problem

don't get though. In the problematic output the lipids can not be one single residue, but should be two or more residues. Berk > Date: Mon, 18 Jan 2010 10:31:19 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] trjconv problem > > &

Re: [gmx-users] trjconv problem

of residues in a lipid. Berk Date: Mon, 18 Jan 2010 13:05:42 -0200 From: stefh...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] trjconv problem I am trying to use trjconv to extract frames from my protein/memb

RE: [gmx-users] trjconv problem

numbering single-residue molecules. If you also want you lipids to continue numbering, you'll have to set the env.var. GMX_MAXRESRENUM to the number of residues in a lipid. Berk Date: Mon, 18 Jan 2010 13:05:42 -0200 From: stefh...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] trjconv pr

[gmx-users] trjconv problem

I am trying to use trjconv to extract frames from my protein/membrane system in order to analyse with gdmat. Before using git's latest gromacs version, everything worked just fine. But now, every coordinate file trjconv gives me has the DPPC lipid molecules without numbering. It is like if my membr

Re: [gmx-users] trjconv problem

Hi, thanks for the tips. First I used the information of the exact time I got from g_cluster which did not work (t=5590.093). So I used trjconv to convert the whole trajectory in a pdb-file from which I got the exact time (t=5590.00049) of the frame to be extracted that was different compared t

Re: [gmx-users] trjconv problem

hi, similar happened to me, when i used the -b and -e flags of trjconv. to me it seemed that if you do not hit exactly the time frame as written in the trr file, trjconv will not output anything. when i used the -dump flag it worked, because then frames near the specified time are dumped. hope

Re: [gmx-users] trjconv problem

Bjoern Windshuegel wrote: Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Se

[gmx-users] trjconv problem

Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Setting output precision to 0.00