[gmx-users] High Temperatures in NVT

Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something wrong with the system or is this normal to see such fluctuations ? There was no warning and the equ

Re: [gmx-users] Salt bridge analysis tool

On 3/14/13 10:14 PM, albielyons wrote: Hi, I am trying to analyse my trajectory for specific salt bridges and the only program I can find is g_saltbr with the -sep command, which gives back all atom pairs that come within the set cutoff at any point in simulation time, whether they are charged

[gmx-users] Salt bridge analysis tool

Hi, I am trying to analyse my trajectory for specific salt bridges and the only program I can find is g_saltbr with the -sep command, which gives back all atom pairs that come within the set cutoff at any point in simulation time, whether they are charged and H-bond partners or not and regardless

RE: [gmx-users] polymer duplicate atoms

The residue number is not incrementing in your coordinate file (it stays as 1), so it thinks it is all the same residue. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

[gmx-users] polymer duplicate atoms

Hi I use the pdb2gmx to generate topology file of polymer f2311(fluororubber) with the incorrect information of GROMACS structural file (conf.gro). There are 680 atoms in my input (.pdb) file. But, 660 atoms are deleted in conf.gro file because of duplicate atoms. The printed message as follow: <

Re: [gmx-users] bonding energy

On 3/14/13 4:08 PM, fatemeh ramezani wrote: I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command: g_dist_mpi -f x.trr -s x.tpr -n index.ndx -o pro.xvg Then I choose the bond option (option 1) from the proposed optio

[gmx-users] bonding energy

I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command: g_dist_mpi  -f   x.trr   -s  x.tpr   -n index.ndx -o pro.xvg Then I choose the bond  option (option 1)  from the  proposed options. Is this true for energy bonding finding betw

[gmx-users] Re: template parallelization

Thanks for the reply . Looks like it is not a layman's problem but the reply u sent me has given me the idea where to start . -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006325.html Sent from the GROMACS Users Forum mailing list archiv

Re: [gmx-users] Re: template parallelization

Gromacs currently use OpenMP and/or MPI with it's own wrappers for parallel computation. There is a general framework being developed for parallelizing analysis tools, but I don't know the specifics and I beleive it's not ready for use yet. Is that helping you? Erik On Mar 14, 2013, at 3:

[gmx-users] Re: template parallelization

Sorry but i can't understand the part about parallelization framework in gromacs . Can you please elaborate on this -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006323.html Sent from the GROMACS Users Forum mailing list archive at Nabb

Re: [gmx-users] template parallelization

Do you really mean compile time? If so, issue make -j X (where x is the number of jobs used for building). If you mean runtime then the easiest thing is to split your trajectory in parts and run the processes in parallel, then patch the results together. That's if the calculations can be do

[gmx-users] Re: TMD using free energy code

I have done a test for a TMD between two conformations of a POPC in water with this mdp file: define = -DPOSRES_TMD ; POSRES-TMD defined in the top file and including only the heavy atom of POPC refcoord-scaling = all cpp= /usr/bin/cpp constraints = hbonds constraint_al

[gmx-users] template parallelization

First, here my system : Cent Os 64 bits gcc : 4.4.6 fftw : 3.3.2 including SSE 2 I am writing a code to find out the number of five and six membered rings in structure I of hydrate . My code takes long time to compile for my 500ps trajectory . So my query is that can the template file be made to r

Re: [gmx-users] query for gromacs-4.5.4

One cannot run an arbitrary simulation on an arbitrary number of processors. The particles in the simulation have to get mapped to processors that handle them. This is done in small parcels called domains. The atoms move between domains, and so the responsibility moves too. If the velocities are hi

[gmx-users] Re: Gromacs-4.6 installation on cygwin problem

Mr M. Thanks a lot for your help... I will contact you if I get any problem. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-4-6-installation-on-cygwin-problem-tp5006297p5006319.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-use

Re: [gmx-users] query for gromacs-4.5.4

Hello Sir, The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than that. 16 proceses : Segmentation fault and For 32 processes it gives : "Fatal error : 467 particles communicated to PME node 4 are more than 2/3 times the cut off out of the domain decomposition cell of their char

Re: [gmx-users] position restraints

Restraints allow, by definition, for slight deviations. Erik On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote: Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-re

[gmx-users] position restraints

Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define =  -DPOSRES to minim.mdp file. After minimization, whe

Re: [gmx-users] MD in Vacuum

Hi, You also need to consider the ensemble you want to investigate. If you simulate under constant energy you need a shorter timestep than you would have in solution and probably double precision. In the articles I list below we used a timestep of 0.5 fs and 1 fs, respectively, and double