Re: [gmx-users] Re: trjconv for pbc

On 11/3/13 7:12 AM, rankinb wrote: That last procedure works. I really appreciate your help. The only other question I have is related to the selection process. Is there a way to select the oxygen atoms of water within a certain distance of a molecule, as well as the corresponding hydrogen a

[gmx-users] Re: trjconv for pbc

That last procedure works. I really appreciate your help. The only other question I have is related to the selection process. Is there a way to select the oxygen atoms of water within a certain distance of a molecule, as well as the corresponding hydrogen atoms on the water molecule? Right now,

Re: [gmx-users] Re: trjconv for pbc

On 11/2/13 12:25 PM, rankinb wrote: Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, th

[gmx-users] Re: trjconv for pbc

Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, the resulting coordination shell configura

[gmx-users] Re: trjconv for pbc

Here is a snapshot of what I was able to extract, if that helps. Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012166.html Sent from the

Re: [gmx-users] Re: trjconv for pbc

On 11/2/13 11:23 AM, rankinb wrote: Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -

[gmx-users] Re: trjconv for pbc

Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains the w

[gmx-users] Re: trjconv center problem

ahh, i thought that the program was "skipping" as in not doing the centering command on certain frames due to one reason or another. Ill look into your suggestion Thank you very much for the help. -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007

Re: [gmx-users] Re: trjconv center problem

On 4/19/13 4:37 PM, Brad Van Oosten wrote: Ahh, yes perhaps i was unclear. The output file also has the same number of steps. Checking file md50_centered.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Ti

[gmx-users] Re: trjconv center problem

Ahh, yes perhaps i was unclear. The output file also has the same number of steps. Checking file md50_centered.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time

Re: [gmx-users] Re: trjconv center problem

On 4/19/13 4:28 PM, Brad Van Oosten wrote: Checking file md50.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500

[gmx-users] Re: trjconv center problem

Checking file md50.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500012 Velocities 0 Forces

Re: [gmx-users] Re: trjconv center problem

On 4/19/13 4:19 PM, Brad Van Oosten wrote: The trajectory file is from a consecutive run so i would hope the frames are evenly spaced. What does gmxcheck tell you? No reason to hope when you can prove conclusively one way or another :) -Justin --

[gmx-users] Re: trjconv center problem

The trajectory file is from a consecutive run so i would hope the frames are evenly spaced. -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007475.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailin

[gmx-users] Re: trjconv centre protein

Crystal clear! Thank you Justin! :) Take care. Regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454p5006459.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] Re: trjconv centre protein

On 3/19/13 8:00 AM, Ewaru wrote: HI Justin, Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the protein has to be in the center (inside the box) before the simulation, is it? Absolutely not. In a periodic system, there is no such thing as a center. Centering within

[gmx-users] Re: trjconv centre protein

HI Justin, Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the protein has to be in the center (inside the box) before the simulation, is it? Thank you. Best regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454

[gmx-users] Re: trjconv -pbc nojump across multiple trajectories

Thanks for your reply, Tsjerk. Indeed, trjcat is a good option. I could first run "trjconv -pbc nojump" on a trajectory, then keep the last frame as a trr and stitch it with the following trajectory; trjconv then takes the first frame as reference for the nojump. Regarding this, what would b

Re: [gmx-users] RE: trjconv -dump problem

On 14/02/2012 11:39 PM, Ehud Schreiber wrote: Dear Mark (or anybody else interested), The .trr file does include the final (t = 217) frame - first, trjconv said: Reading frame 3 time 217.000 and second this is verified by converting the whole trajectory to .gro: trjconv -f 1IARcompleted_W

[gmx-users] RE: trjconv -dump problem

Dear Mark (or anybody else interested), The .trr file does include the final (t = 217) frame - first, trjconv said: Reading frame 3 time 217.000 and second this is verified by converting the whole trajectory to .gro: trjconv -f 1IARcompleted_WT_minimized.trr -s 1IARcompleted_WT_minimized.tp

Re: [gmx-users] Re: trjconv with multiple chains

On 10/01/11 08:43, yuanyuan wang wrote: sorry to say I can not found a center for the trj. I tried to make bigger box by trjconv -box -boxcenter, but it seems that the trj only exist in the old box area ,bigger box cannot stop jumps. Is it really happened that I can do nothing with it ? yuanyuan

Re: [gmx-users] Re: trjconv with multiple chains

On 01/10/11, yuanyuan wang wrote: > sorry to say I can not found a center for the trj.  I tried to make bigger > box by trjconv -box -boxcenter, but it seems that the trj only exist in the > old box area ,bigger box cannot stop jumps. > > Is it really happened that I can do nothing with it ?

[gmx-users] Re: trjconv with multiple chains

sorry to say I can not found a center for the trj. I tried to make bigger box by trjconv -box -boxcenter, but it seems that the trj only exist in the old box area ,bigger box cannot stop jumps. Is it really happened that I can do nothing with it ? yua

Re: [gmx-users] Re: trjconv

mohsen ramezanpour wrote: It is surprising!, Because I used -sep option But it made 20 pdb file separately with 0 byte! Do you have sufficient disk space? The only way I can see that you would get files of zero bytes are: 1. Not enough space on the disk 2. The frames specified do not ex

Re: [gmx-users] Re: trjconv

Dear Vitaly rerunning my program take a long time(approximately 12 days),besides I checked my trojectories and it was completed On Sun, Nov 7, 2010 at 9:12 PM, Vitaly Chaban wrote: > Did you try to re-run your trajectory? Does the problem persist then? > > > > > I have a trajectory with 2 fr

Re: [gmx-users] Re: trjconv

It is surprising!, Because I used -sep option But it made 20 pdb file separately with 0 byte! On Mon, Nov 8, 2010 at 11:26 AM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > of course I could generate a pdb file without -b and -e options,but I don't > want it. > > besides I did the

Re: [gmx-users] Re: trjconv

of course I could generate a pdb file without -b and -e options,but I don't want it. besides I did the same process with xtc file and I resulted in a 0 byte file :( On Mon, Nov 8, 2010 at 11:21 AM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear justin > > I checked what you sa

Re: [gmx-users] Re: trjconv

Dear justin I checked what you said,yes,both of them(trr and xtc files) were completely done as I wanted in my mdp file. what is your points of view? On Sun, Nov 7, 2010 at 9:15 PM, Justin A. Lemkul wrote: > > > Vitaly Chaban wrote: > >> Did you try to re-run your trajectory? Does the problem

Re: [gmx-users] Re: trjconv

Vitaly Chaban wrote: Did you try to re-run your trajectory? Does the problem persist then? Perhaps the faster solution would be to see what gmxcheck says about the trajectory. -Justin I have a trajectory with 2 frames. i want to separate just 1000 last frames of it in pdb formt an

[gmx-users] Re: trjconv

Did you try to re-run your trajectory? Does the problem persist then? > I have a trajectory with 2 frames. > i want to separate just 1000 last frames of it in pdb formt and 1000 first > frames too. > I entered this command: > trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000 > >

[gmx-users] Re: trjconv index file

I assume you meant to send this to the list, so I will CC the message there. Rabab Toubar wrote: Hi Trying to extract the protein from the md run without waters, all the mailing lists suggests using an index file before running trjconv, but I get file input/output error Can someone give me m

RE: [gmx-users] RE: trjconv problem

@gromacs.org Subject: [gmx-users] RE: trjconv problem Hi, It is not a pdb2gmx feature, but a global one. pdb2gmx is only affected in the sense that it retains the residue numbers from the input pdb. I assume those will be different for most lipid pdb files (if you use pdb2gmx for those

[gmx-users] RE: trjconv problem

> > > Hi, > > It is not a pdb2gmx feature, but a global one. > pdb2gmx is only affected in the sense that it retains the residue numbers > from the input pdb. > I assume those will be different for most lipid pdb files (if you use > pdb2gmx for those). > This renumbering is done by any program that

Re: [gmx-users] Re: trjconv error

You seem not to get it... I specifically chew out for you that you need to give a listing using the command ls -l. That will also show what the size of the file is. This is completely pointless this way! Also, you only now state the command you gave. Now, rereading the first mail, it also said ..t

[gmx-users] Re: trjconv error

> Message: 2 > Date: Wed, 27 Aug 2008 15:31:58 +0530 (IST) > From: [EMAIL PROTECTED] > Subject: [gmx-users] trjconv error > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Tsjerk > > we have checked it., but of no use it giving some

[gmx-users] Re: trjconv help

sarbani chattopadhyay wrote: hi, I had run MD simulations where the output control parameters were nstxout=250 nstvout= 1000 nstenergy=100 Due to this the '.trr' file is very large. I want to compress this file so that xyz coordinates are stored every 1000 steps, velo