Re: [gmx-users] using more processors for g_mindist

Mark, i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. Thanks On Wed, Feb 29, 2012 at 12

[gmx-users] error

Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more information and tips for troubleshooting, please c

Re: [gmx-users] using more processors for g_mindist

On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein a

Re: [gmx-users] error

On 29/02/2012 7:28 PM, RAMYA NAGA wrote: Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more inf

[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Hi, I have Gromacs-GPU version 4.5.5 and GTX 580. I ran dhfr-solv-PME benchmark test (see below) and my run was killed after couple of hours exhausting all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What is wrong? Thanks, Efrat > mdrun-gpu -dev

Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 185

c boundary conditions > pbc= xyz; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres; account for cut-off vdW scheme > ; Velocity generation > gen_vel= yes; assign velocities from Maxwell distributionchanged > gen_temp= 400

RE: [gmx-users] error

try: $ df -h . And see how much quota you have available. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of RAMYA NAGA [nagra...@gmail.com] Sent: Wednesday, February 29, 2012 8:28 AM To: Discussion list for GROMACS user

Re: [gmx-users] using more processors for g_mindist

Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>I run energy minimization of my protein with implicit solvent: >>

[gmx-users] using g_angle

Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is in

Re: [gmx-users] Positive Coul. recip. term

On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: > The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and > the force field is from Lopes (CLaP). I tried deleting all of the > cation dihedrals from the itp file and found that the run did not > crash, although it still had a posit

[gmx-users] quick question about restart

Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

On 29/02/2012 9:26 PM, Steven Neumann wrote: On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] quick question about restart

On 29/02/2012 9:47 PM, Anna Marabotti wrote: Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation

Re: [gmx-users] using g_angle

On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. However it produces a .xvg file whe

Re: [gmx-users] using more processors for g_mindist

On 29/02/2012 9:05 PM, aiswarya pawar wrote: Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist What makes you think there is only one atom satisfying that cutoff? 5.00e+02 518 42680 5.01e+02

Re: [gmx-users] md in vacuo

On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: Dear GROMACS community, I use the following parameters to run MD of ethane in vacuo. Then I calculate the H-C-C-H dihedral angle distribution and from that the rotational energy barrier using the formula DeltG=-k*T*ln(x), where x is the dihedra

Re: [gmx-users] using g_angle

2012/2/29 Mark Abraham : > On 29/02/2012 9:39 PM, francesca vitalini wrote: >> >> Hi all, >> I'm trying to use g_angle to calculate a list of dihedrals that I have >> into an hand made index file (angles.ndx), which looks like >> [ dihedrals ] >> 2 5 9 10 >> 10 15 18 19 >> . > > > mk_angndx mig

Re: [gmx-users] using g_angle

hi francesca, i think what you are looking for is this g_sgangle $indexFile -f $traj -s $tpr -oa $outfile before that, you have to define two planes (by 3 atom indices each) in your index file [ dihed1 ] 523 680 3482 [ dihed2 ] 680 3482 3691 which you choose when having started g_sgangle.

Re: [gmx-users] using g_angle

On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abraham: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 1

Re: [gmx-users] mdrun -pd

On 1/03/2012 12:31 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to use option -p of mdrun for particle decomposition. I used: mpiexec mdrun -pd -deffnm nvt I obtain: apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead

Re: [gmx-users] mdrun -pd

On Wed, Feb 29, 2012 at 1:47 PM, Mark Abraham wrote: > On 1/03/2012 12:31 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> I am trying to use option -p of mdrun for particle decomposition. >> I used: >> >> mpiexec mdrun -pd -deffnm nvt >> >> I obtain: >> >> apps/intel/ict/mpi/3.1.038/**bin/mpdli

Re: [gmx-users] using g_angle

Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 then if I use the command line g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov a

Re: [gmx-users] using g_angle

On 1/03/2012 1:00 AM, francesca vitalini wrote: Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 I said in my last email that my s

Re: [gmx-users] md in vacuo

On 29 February 2012 14:04, Mark Abraham wrote: > On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: > > Dear GROMACS community, > > I use the following parameters to run MD of ethane in vacuo. Then I > calculate the H-C-C-H dihedral angle distribution and from that the > rotational energy barrier

Re: [gmx-users] using g_angle

Thank you. It worked now. Best Francesca 2012/2/29 Mark Abraham : > On 1/03/2012 1:00 AM, francesca vitalini wrote: >> >> Hi Mark, >> Thanks for your answer. What I'm trying to do is calculate the value >> in degrees of  the angles listed in my index file. If my index file >> looks like >> [ dih

Re: [gmx-users] PBC - Protein and Ligands

Steven Neumann wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr -pbc

Re: [gmx-users] PBC - Protein and Ligands

On 1 Mar, 2012, at 1:01, Steven Neumann wrote: > Dear Gmx Users, > > I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The > problem I face is PBC which I cannot get rid of. I used: > > 1. First make your molecules whole if you want them whole (system). > trjconv -

Re: [gmx-users] PBC - Protein and Ligands

i always did it (successfully) with one single command: trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx regards vedat Am 29.02.2012 18:01, schrieb Steven Neumann: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. T

Re: [gmx-users] Positive Coul. recip. term

The parameters I used are from the following reference: Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 This paper gives the bonded parameters of the anion and the non-bonded parameters of both ions. The bonded parameters of the cation were obtained (as indicated in the reference abo

Re: [gmx-users] Positive Coul. recip. term

On Wed, 2012-02-29 at 11:12 -0700, Denny Frost wrote: > The parameters I used are from the following reference: > > Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 > > > This paper gives the bonded parameters of the anion and the non-bonded > parameters of both ions. The bonded para

RE: [gmx-users] quick question about restart

I use the second option there on all my simulations, using a script. Simulations are done in 10ns blocks, at the completion of that the pbs script submits the next job. Have found this way much less hassle, better computer utilisation etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and

[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield

Dear Gromacs User and developers: Please help with 2 questions: 1) Does the converted charmm forcefield (charmm36 or 27) in gromacs include forcefield parameters for carbohydrate (sugar)? I looked through *itp and can not find them in converted charmm36 and 27 in gromacs. 2) How to convert charm

Re: [gmx-users] how to use charmm ff in gmx and carbohydrate forcefield

On 2012-02-29 05:11:48PM -0600, Tom wrote: > Dear Gromacs User and developers: > > Please help with 2 questions: > 1) Does the converted charmm forcefield (charmm36 or 27) in gromacs > include forcefield parameters for carbohydrate (sugar)? I looked > through *itp and can not find them in convert

[gmx-users] on the dissociation of protein complex during MD

Dear All,   Some of the complexes of PDB files in RCSB are not from protein-protein interaction, but from the packing of protein crystal. Thus in solution the "protien complex" may dissociate.   However as for the protein are usually very large, and I regard it is difficult to observe that 2 (or

Re: [gmx-users] on the dissociation of protein complex during MD

On 1/03/2012 11:57 AM, Dialing Pretty wrote: Dear All, Some of the complexes of PDB files in RCSB are not from protein-protein interaction, but from the packing of protein crystal. Thus in solution the "protien complex" may dissociate. However as for the protein are usually very large, and I re

[gmx-users] dihedral distributions

Hi all, Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system? g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the time interval -b to -e ? -- Thanks, J. --

[gmx-users] crashed run...

Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time of crash?? What is the process for to start

Re: [gmx-users] crashed run...

On 1/03/2012 5:30 PM, rama david wrote: Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time

Re: [gmx-users] dihedral distributions

On 1/03/2012 5:07 PM, Juliette N. wrote: Hi all, Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system? g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the