[gmx-users] Regarding parallel run in Gromacs 5.0

​​Dear All I have upgraded my Gromacs v4.5.5 to 5.0. I am unable to run parallel minimization and simulation in cluster. Previously (v4.5.5) I was simulating using the command “mdrun –v –s em.tpr –nt 30 &” and thus assigning 30 CPU’s for the system. However, in the new version it is not working, a

[gmx-users] using g_hbond between index gps of specific interest

Hello everyone, I am re sending my mail since I did not understand the suggestion provided last time. I want to calculate the effect of incorporating ions in the grooves and backbones of a double stranded DNA molecule in the hydrogen bonding between the two chains constituti

[gmx-users] MDP parameters for OPLS-aa + Verlet cutoff scheme

Hi everyone, I would like to run some protein simulations using the OPLS-aa forcefield and I'm wondering what would the "correct" parameters be. Is there a set of agreed-upon parameters that are safe to use? After some research I found a set of parameters here: https://github.com/orbeckst/Grom

Re: [gmx-users] How can I analyze an interaction between protein and CU ions

Dear gmx_users, How can I analyze an interaction between protein and CU ions? Regards, Batsaikhan On Thursday, December 4, 2014 1:46 PM, Batdorj Batsaikhan wrote: Dear gmx_users, How can I analyze an interaction between protein and CU ions? Regards, Batsaikhan -- Gromacs Use

Re: [gmx-users] Errors about dihidral angle type 9 in free energy perturbation

Thanks Justin for your reply. Actually we have modified ffbonded.itp to include the state B parameters for dihedral function type 9, but they are not recognized by GROMACS. We did not get any error when using gmx4.0.4 and amber99sb, in which dihedral type 3 (RB) is used.  We get the error onl

Re: [gmx-users] Performance of GPU Workstation (GPU selection)

Zitat von Carsten Kutzner : Are you planning to run a single copy of that MD system across the 4 GPUs? I am not sure that this will scale well. I have benchmarked a ~8 atom test system on a dual processor E5-2670v2 (altogether 20 physical cores on a node @ 2.5 GHz) with 4x GTX 780Ti, wh

[gmx-users] biasing potential replica exchang for polymer

Dear gromacs users, I am using 16 replicas with different dihedral potential for peptide in explictit solvet. for 20 ns I got this result: Replica exchange statistics Repl attempts, 5000 odd, 4999 even Repl average probabilities: Repl 0123456789 1

Re: [gmx-users] charmm to gromacs

On 12/4/14 1:59 PM, Rebeca García Fandiño wrote: Dear Gromacs users, I am trying to obtain the .itp files for an organic molecule for a MD simulation in GROMACS using the CHARMM force field. I am trying to use cgenff_charmm2gmx.py: python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str char

[gmx-users] charmm to gromacs

Dear Gromacs users, I am trying to obtain the .itp files for an organic molecule for a MD simulation in GROMACS using the CHARMM force field. I am trying to use cgenff_charmm2gmx.py: python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str charmm36-nov2014.ff After this step, I obtain several fi

Re: [gmx-users] Performance of GPU Workstation (GPU selection)

Hi, On 03 Dec 2014, at 22:12, m...@2718-mail.de wrote: > Dear gromacs Users, > > We are currently considering to build a GPU Workstation for Gromacs > Simulations. > > Our typical Systems consist of ~3000 Atoms(~30 per Molecule) solvated in > 1-4 tip4p water molecules. > > > We tho

Re: [gmx-users] use of g_hbond

Dear Alex, as you can see in my previous mail, I have made groups in the index files using make_ndx (gp no 10-17). My question is with the kind of groups I have, how can I calculate H bonding between chain A and chain B in presence of sodium . Should I merge gp 13 and 2 together and ma

[gmx-users] g_covar + g_anaeig entropy calculation

Hello: I am trying to calculate ligand binding energy for protein/ligand system. The enthapy part was done by GMXPBSA. Now I would like to evalutate the entropy part with g_covar + g_anaeig. Here I got some questions: --- is it necessary using double precison Gromacs for entropy evaluation?

Re: [gmx-users] Errors about dihidral angle type 9 in free energy perturbation

On 12/4/14 2:32 AM, Jianguo Li wrote: Dear All, I am trying to use free energy perturbation module of gromacs to do hamiltonian replica exchange using CHARMM27 all-atom force field (with CMAP) - version 2.0 I am using 4.5.4 version of gromacs according to manual (Table 5.5), it allows to per

Re: [gmx-users] (no subject)

On 12/4/14 5:09 AM, Prajisha Sujaya wrote: i have one doubt whiling performing dynamics for ribosomal proteins, it consists of 21 proteins with different length. i have modeled and joined together as whole pdb. while performing dynamics using gromacs in nvt step im getting error segmenuted dum

Re: [gmx-users] g_spatial

On 12/4/14 3:47 AM, pratibha kapoor wrote: Hi, I would like to calculate spatial distribution function of my cosolvent molecules around peptides. I am using g_spatial tool. I have removed periodicity, rotational and translational motion of my solute as suggested in the manual. grid.cube file w

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15

On 12/4/14 6:54 AM, soumadwip ghosh wrote: Dear Alex, as you can see in my previous mail, I have made groups in the index files using make_ndx (gp no 10-17). My question is with the kind of groups I have, how can I calculate H bonding between chain A and chain B in presence of sod

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15

Dear Alex, as you can see in my previous mail, I have made groups in the index files using make_ndx (gp no 10-17). My question is with the kind of groups I have, how can I calculate H bonding between chain A and chain B in presence of sodium . Should I merge gp 13 and 2 together and ma

Re: [gmx-users] energy groups rerun from reduced xtc file

On Thu, Dec 4, 2014 at 10:16 AM, Harry Mark Greenblatt < harry.greenbl...@weizmann.ac.il> wrote: > BS"D > > Dear All, > >In an attempt to save disk space while using longer simulations of a > DNA + Protein + solvent system, > I had mdrun create an xtc file with only the DNA, Protein, and ions,

Re: [gmx-users] Umbrella Sampling continuation

Dear Alexander, As you used -deffnm umbrella0, you should have a file umbrella0.cpt insted of state.cpt which allows you to restart the calculation. Regards, lalita On Thu, Dec 4, 2014 at 10:17 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailin

[gmx-users] (no subject)

i have one doubt whiling performing dynamics for ribosomal proteins, it consists of 21 proteins with different length. i have modeled and joined together as whole pdb. while performing dynamics using gromacs in nvt step im getting error segmenuted dumped. in that file im getting step.pdb. How to o

[gmx-users] g_covar + g_anaeig entropy calculation

Hello: I am trying to calculate ligand binding energy for protein/ligand system. The enthapy part was done by GMXPBSA. Now I would like to evalutate the entropy part with g_covar + g_anaeig. Here I got some questions: --- is it necessary using double precison Gromacs for entropy evaluation?

[gmx-users] energy groups rerun from reduced xtc file

BS"D Dear All, In an attempt to save disk space while using longer simulations of a DNA + Protein + solvent system, I had mdrun create an xtc file with only the DNA, Protein, and ions, excluding the water molecules. No trr file was produced. This is fine for many things, but since I also wa

[gmx-users] g_spatial

Hi, I would like to calculate spatial distribution function of my cosolvent molecules around peptides. I am using g_spatial tool. I have removed periodicity, rotational and translational motion of my solute as suggested in the manual. grid.cube file was generated after using g_spatial command. But

[gmx-users] Errors about dihidral angle type 9 in free energy perturbation

Dear All, I am trying to use free energy perturbation module of gromacs to do hamiltonian replica exchange using CHARMM27 all-atom force field (with CMAP) - version 2.0 I am using 4.5.4 version of gromacs according to manual (Table 5.5), it allows to perturb dihedral angles: proper dih. multi,