Re: [gmx-users] tpbconv and tpr file problem...

Thanks On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham wrote: > On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: > > > On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote: > >> On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: >> >>> Hi Users: >>> >>> I was trying to calculate the energy c

Re: [gmx-users] tpbconv and tpr file problem...

On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham > wrote: On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: Hi Users: I was trying to calculate the energy contribution of an specif

Re: [gmx-users] tpbconv and tpr file problem...

On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote: > On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: > >> Hi Users: >> >> I was trying to calculate the energy contribution of an specific ion in >> my simulation. After extract a given frame from the simulation, I >> recalculate the energies o

Re: [gmx-users] tpbconv and tpr file problem...

On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to

[gmx-users] tpbconv and tpr file problem...

Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to create a new gro file and a new tpr without the ion. I t

Re: [gmx-users] tpbconv to extend a simulation

Juliette N. wrote: Hello all, I read the online instruction on how to extend a run. I just wanted to double check the procedure because of the NOTE below after issuing tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 1 NOTE: Reading the state from trajectory is an obsole

[gmx-users] tpbconv to extend a simulation

Hello all, I read the online instruction on how to extend a run. I just wanted to double check the procedure because of the NOTE below after issuing tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 1 NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.  

[gmx-users] tpbconv - segmantation fault

Hi I'm trying to set to zero the charges of my ligand group (MOL) using tpbconv: tpbconv_d -s md.tpr -f md.trr -n -o md_lig_zero.tpr -zeroq then I select the MOL group and I get the following message: Selected 14: 'MOL' Segmentation fault (core dumped) Any explanation to why this may have happ

Re: [gmx-users] tpbconv question

Hi Marc, I think that -zeroq ignores the indexing. Using an index will extract a .tpr for the index group only, which is not what you want. There is no simple way to do what you want (using tpbconv). You'll have to modify the charge in the .top file and generate a new .tpr Cheers, Tsjerk On Sep

[gmx-users] tpbconv question

Hello, I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following: [mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq

[gmx-users] tpbconv extension

Dear Gromacs users, I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interfa

Re: [gmx-users] tpbconv -zeroq results all coulombic energies to zero

On 2010-12-03 08.45, BIN ZHANG wrote: Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are

[gmx-users] tpbconv -zeroq results all coulombic energies to zero

Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are zeros, i.e., Coulomb-(SR), Coul.-r

Re: [gmx-users] tpbconv subset

John Shultz wrote: I modified the .mdp file, created a full system tpr, then ran it through tpbconv, then ran mdrun using the original xtc. It says the atom numbers don't match. mdrun -rerun md.xtc -v -s lig.tpr --- Program mdrun, VERSION 4.

Re: [gmx-users] tpbconv subset

I modified the .mdp file, created a full system tpr, then ran it through tpbconv, then ran mdrun using the original xtc. It says the atom numbers don't match. mdrun -rerun md.xtc -v -s lig.tpr --- Program mdrun, VERSION 4.0.5 Source code file: m

Re: [gmx-users] tpbconv subset

John Shultz wrote: Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? Modify the .mdp file the way you need to, create a full-system .tpr fi

Re: [gmx-users] tpbconv subset

Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> I want

Re: [gmx-users] tpbconv subset

John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backw

[gmx-users] tpbconv subset

I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file fo

Re: [gmx-users] tpbconv*

sudheer babu wrote: > Hi users, > I am running membrane protein simulation in between system crashed due to > power fluctuations, I am trying to extend this run by using tpbconv command > tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr > it showed that > > Reading toplogy and shit from 1ns_

Re: [gmx-users] tpbconv*

sudheer babu wrote: Hi users, I am running membrane protein simulation in between system crashed due to power fluctuations, I am trying to extend this run by using tpbconv command tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr it showed that Reading toplogy and shit from 1ns_2timeTh

[gmx-users] tpbconv*

Hi users, I am running membrane protein simulation in between system crashed due to power fluctuations, I am trying to extend this run by using tpbconv command tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr it showed that Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr Reading file

Re: [gmx-users] tpbconv functionality

Hi Cesar, Not with tpbconv. You can do it with grompp, adding the .trr end .edr file you have as input and making sure that you don't generate new velocities and set unconstrained_start to yes. Cheers, Tsjerk On Sun, Jun 29, 2008 at 10:18 PM, Cesar Avila <[EMAIL PROTECTED]> wrote: > I found the

[gmx-users] tpbconv functionality

I found the tpbconv tool very usefull for generating tpr files for resuming the simulations. Nevertheless I couldn't find an option to set/change the number of processors to use as the -np option in grompp. Is there a way to do this? ___ gmx-users mailin

Re: [gmx-users] tpbconv restart crashing on 3.3.1

rs Sent: Sunday, June 10, 2007 4:15:29 PM Subject: Re: [gmx-users] tpbconv restart crashing on 3.3.1 Alan Dodd wrote: > Hello all, > A recent simulation has been running on a cluster for a couple of weeks. > 5.something-ns in it crashed due to a hardware glitch. All perfectly &g

Re: [gmx-users] tpbconv restart crashing on 3.3.1

Alan Dodd wrote: Hello all, A recent simulation has been running on a cluster for a couple of weeks. 5.something-ns in it crashed due to a hardware glitch. All perfectly understandable so far. The strange thing is, using tpbconv now results in a .tpr that crashes in the first step due to mas

Re: [gmx-users] tpbconv restart crashing on 3.3.1

Lars Schaefer wrote: Hi Alan, if your trajectory and energy files are OK, my guess is that the tpr file is corrupted. Use gmxdump all round and see what is going on. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

Re: [gmx-users] tpbconv restart crashing on 3.3.1

Hi Alan, if your trajectory and energy files are OK, my guess is that the tpr file is corrupted. Lars Alan Dodd wrote: Hello all, A recent simulation has been running on a cluster for a couple of weeks. 5.something-ns in it crashed due to a hardware glitch. All perfectly understandable so

[gmx-users] tpbconv restart crashing on 3.3.1

Hello all, A recent simulation has been running on a cluster for a couple of weeks. 5.something-ns in it crashed due to a hardware glitch. All perfectly understandable so far. The strange thing is, using tpbconv now results in a .tpr that crashes in the first step due to massive LINCS errors.

Re: [gmx-users] tpbconv

I was running a parallel MD simulation, the program stopped (no more output data) in the middle without any error message in the log file. When I use command "top" to check the process, the output message showed the program was still running, but no more output data. Therefore I killed the jo

[gmx-users] tpbconv

Hello, GMX users, I was running a parallel MD simulation, the program stopped (no more output data) in the middle without any error message in the log file. When I use command "top" to check the process, the output message showed the program was still running, but no more output data. Therefore I

[gmx-users] tpbconv inexact restart due to nstxout!=nstenergy?

Hello, I have a 10ns trajectory and also a 5ns trajectory restarted from the 5ns point in the original trajectory. However, the runs diverge almost immediately (as judged by g_dist selecting one Calpha and one water molecule). The ensemble was NPT with PME electrostatics nstlist = 10