Re: [gmx-users] joining line in rms

Hi, Though it's not Gromacs related, it seems like you put two set of data into one (e.g. joining two sets of RMSf in one file). If this is the case put them in two files or in two columns of the same file and using -nxy option (assuming you're using Grace). Anyway, consulting manual of your plot

[gmx-users] Energy minimisation goes to several values

Dear Users, I am energy minimising a quite large solvated system containing protein and lipids (~800,000 atoms). I used to fix components of the system in order to speed-up energy minimisation and sometimes it is easier to debug such processes. Here is my protocol: 1. fix all except water and so t

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

Yes, I just wanted to try the script, to figure out what's hapenning.. I tried both N4 and O11. Sure.I'll do that. Thank you in advance On Fri, Jun 26, 2015 at 3:10 AM, Justin Lemkul wrote: > > > On 6/25/15 6:12 PM, Mahboobe Sadr wrote: > >> I used spc water and the command was : >> >> perl

Re: [gmx-users] Simulation of polarizable Carbon nanotubes

On 6/25/15 6:21 PM, S.M. Golam Mortuza wrote: Hi Justin, Thanks a lot for your reply and suggestion. I have pulled the master branch and performed "git checkout drude". I think, the file named md.cpp in /src/program/mdrun is the main file to run the code. Please let me know if I am wrong. T

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

On 6/25/15 6:12 PM, Mahboobe Sadr wrote: I used spc water and the command was : perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref N4 -middle C50 -water 3 -v yes Using N4 as a reference is a bad idea; you don't want to desolvate the headgroups. This will lead to unstable si

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

On 6/25/15 2:46 PM, John Degenstein wrote: Justin, Ok, so I decided to take a different path to solve this issue. Essentially, using the Berendsen Pcoupl the system should condense under high pressure. For some reason it does not seem to work very quickly at least. To get around this issue I r

Re: [gmx-users] Protein-DNA simulation LINKS error

On 6/25/15 3:43 AM, Timofey Tyugashev wrote: Looking through the paper for the FF I see that the values specified are 1.0 nm and 1.05 nm for cutoffs. If I used longer cutoffs than specified, then why it should affect the systme in a deleterious way? Force fields behave unexpectedly when you

Re: [gmx-users] Simulation of polarizable Carbon nanotubes

Hi Justin, Thanks a lot for your reply and suggestion. I have pulled the master branch and performed "git checkout drude". I think, the file named md.cpp in /src/program/mdrun is the main file to run the code. Please let me know if I am wrong. I am just wondering how can I execute the code in my

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

I used spc water and the command was : perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref N4 -middle C50 -water 3 -v yes Regards M.Sadr On Thu, Jun 25, 2015 at 4:50 AM, Justin Lemkul wrote: > > > On 6/24/15 8:53 AM, Mahboobe Sadr wrote: > >> I tried this script with ref atom O1

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

Justin, Ok, so I decided to take a different path to solve this issue. Essentially, using the Berendsen Pcoupl the system should condense under high pressure. For some reason it does not seem to work very quickly at least. To get around this issue I running several steps of equilibration EM follow

Re: [gmx-users] Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format'

OK, that suggests the file itself is fine. 5000fs per frame times 4000 frames is suspiciously close to 2^31... might there be a 32-bit limitation going on here? Otherwise, use trjconv to chop up your trajectory and get access to it that way. Mark On Thu, Jun 25, 2015 at 5:01 PM Vidyalakshmi CM w

Re: [gmx-users] Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format'

Dear Sir, I used the gromacs gmxcheck command and I got the following output display: Item#frames Timestep (ps) Step 48405 Time 48405 Lambda 0 Coords48405 Velocities 0 Forces 0 Box 48405 Therefore the total num

Re: [gmx-users] Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format'

Hi, You can use gmxcheck / gmx check to examine the file and perhaps get some more information, but this sounds like something has mis-managed your file. e.g. you didn't construct it how you think you did, or the (parallel) file system upon which you ran mdrun is not reliable. Mark On Thu, Jun 2

Re: [gmx-users] problem to restart REMD

Thanks very much. Ok I will check again, it seems that they are at the same step! only the thing that comes to my mind is that I used different number of cpus when I tried to update few steps for some replicas, and then I used the primary numbers of cpu that I used. Also I got this error when I up

Re: [gmx-users] problem to restart REMD

Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7ffc783af760, count=4, MPI_DOUBLE,

Re: [gmx-users] problem to restart REMD

Hi, I can't tell either. Please run gmxcheck on all your input files, to check the simulation part, time and step number are all what you think they are (and that they match across the simulations) and try again. Mark On Thu, Jun 25, 2015 at 4:12 PM leila salimi wrote: > Dear Mark, > > When I

[gmx-users] Displacements of the components of the proteinn residue wise for the first eigenvector

hello every one, Actually i want to calculate ​Displacements of the components of the proteinn residue wise for the first eigenvector in gromacs. is thre is any option already present in gromacs for such calculation. thanks in advance-- -- *Rajan kumar choudhary* *Senior Research Fellow* *Depa

[gmx-users] (no subject)

​hello every one, Actually i want to calculate ​Displacements of the components of the proteinn residue wise for the first eigenvector in gromacs. is thre is any option already present in gromacs for such calculation. thanks in advance-- *Rajan kumar choudhary* *Senior Research Fellow* *Departm

[gmx-users] Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format'

Dear All, I am trying to visualize the gromacs output .xtc trajectory on VMD. I am generating .xtc trajectory frames every 5 ps. The total simulation run time is 24195 ps which should give me 4839 frames (without any skip). However, when I load frames say 4000 to 4100, I get the error message 'Err

Re: [gmx-users] How can I use template.c to calculate single point energy?

Dear Mark: Thank you very much for your reply, now the problem has been solved. I write all configurations into a .xtc file and generate a .tpr with the first configurature, then carry out the rerun job, that's the solution. Thank you again! Sincerely! -- Zidan Zhang Ph.D. Candidate Departmen

Re: [gmx-users] Fwd: i want to use water_detetor.pl script

I used spc water and the command was : perl water_deletor.pl -in bilayer.gro -out bilayer_fix.gro -ref N4 -middle C50 -water 3 -v yes Regards M.Sadr On Thu, Jun 25, 2015 at 4:50 AM, Justin Lemkul wrote: > > > On 6/24/15 8:53 AM, Mahboobe Sadr wrote: > >> I tried this script with ref atom O1

[gmx-users] joining line in rms

Hi all, I have been running a dimer in simulation in GROMACS opls/aa, after that I am getting a joining line in the rms fluctuation. anyone please help me for that. chains are separated by A and B nomenclature Please find the plot in the following link https://drive.google.com/file/d/0B7TB1kZS

[gmx-users] 5.0 Benchmark

Hello I was looking for GROMACS benchmarks and I saw the new 5.0 benchmark results at: http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf >From a quick read there aren't many details about the benchmarks themselves. Are the scripts and data used for these runs publicly availa

Re: [gmx-users] Protein-DNA simulation LINKS error

Just to make sure I want to recheck myself: Lennard-Jones interactions cutoffs (set at 10A in the paper) are defined by rvdw short-range electrostatic interactions (set at 10A in the paper two) are defined by rlist and rcoulomb, but when I use Verlet scheme, rlist is ignored anyway. long-range

Re: [gmx-users] The pullf.xvg and pullx.xvg files

Ok thanks! I will analyze this more deeply and maybe also try differen geometries. And sorry for the stupid question, I was reading force but was thinking potential instead... Laura -Original Message- From: "Justin Lemkul" Sent: ‎25/‎06/‎2015 02:23 To: "gmx-us...@gromacs.org" Subject:

[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

Dear Mark: > I think you will need to use a 64 bit mingw with GROMACS 5 and up. Thank you for the comments. I'd tried MinGW-64 (acturally TDM-GCC-64) and succeeded to build 64bit gromacs-5.0.5 on a windows PC. However, I need 32bit gromacs-5.0.5 binary for 32bit windows PCs. Then, I'd tried "-m32

Re: [gmx-users] Protein-DNA simulation LINKS error

Looking through the paper for the FF I see that the values specified are 1.0 nm and 1.05 nm for cutoffs. If I used longer cutoffs than specified, then why it should affect the systme in a deleterious way? Anyway, now I'll try simulations with values from the paper, both for oxoguanine and plai

Re: [gmx-users] How can I use template.c to calculate single point energy?

Hi, On Thu, Jun 25, 2015 at 7:23 AM 张紫丹 wrote: > Dear GROMACS users: > Is it possible to use template.c to calculate single point energy? No. > I know template.c can analyze the trajectory information. Now I want to > calculate a specific system, which contains several configurations > gener

[gmx-users] Free energy, domain decomposition and gmx 465 v 505

Hi all I am running some free energy tutorial calculations to learn more about how those are set up in gromacs, but have run into a problem when using different versions. I am following the free energy tutorial on the Gromacs website (fe-tutorial-4.6), so not Justin's tutorial. With vmx 4.6.5 ev