Re: [gmx-users] g_msd problem

On 5/18/13 4:32 PM, rajat desikan wrote: I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 45 particles, Gromos 54A7 ff) with data stored every ps. g_msd

Re: [gmx-users] g_msd problem

I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 45 particles, Gromos 54A7 ff) with data stored every ps. g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tp

[gmx-users] g_msd problem

Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown below:

[gmx-users] RE: gmx-users Digest, Vol 109, Issue 112

Dear all, I am using g_msd to calculate diffusion coefficient of the centre of mass of single polymer chain with the following command: g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40 However, it often get killed for number of beads larger than 37, as shown bel

Re: [gmx-users] Re: REMD analysis

On Sat, May 18, 2013 at 5:17 PM, bharat gupta wrote: > Dear Sir, > > My main objective of carrying out REMD is to study peptide folding and if > possible to get some insight in protein design and folding. I read some > articles related to my work and they always show temp (replica_index) > graphs

Aw: Re: [gmx-users] Expanding a .top file to have all connection information

  Or just do it by hand and replace the lines in the .top with each protein chains .itp file.   Stephan Gesendet: Freitag, 17. Mai 2013 um 16:17 Uhr Von: "Mark Abraham" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Expanding a .top file to have all connection information

Re: [gmx-users] Add CS ions to system

On 5/18/13 10:02 AM, Shima Arasteh wrote: Hi all, I want to add CS ions to my system by genion but it seems impossible when go through the EM. The molecule section in my top file is: Protein_chain_A 1 Protein_chain_B 1 POPC238 SOL 20406 NA 681 CL

Re: [gmx-users] Re: Running Pull Code

On 5/18/13 1:23 AM, Shima Arasteh wrote: If I skip the pulling code step, how could I generate configurations while there are one ion in each window? Am I supposed to save my favorite snapshots during MD simulation trajectory? You can generate configurations in any way you see fit. SMD is

Re: [gmx-users] charmm in gromacs cut-offs

On 5/18/13 7:58 AM, tarak karmakar wrote: Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already

[gmx-users] Re: proceed from output of MD

Hey, I have figured that out! My bad! :D Thank you. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/proceed-from-output-of-MD-tp5008364p5008368.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g

Re: [gmx-users] Re: REMD analysis

Dear Sir, My main objective of carrying out REMD is to study peptide folding and if possible to get some insight in protein design and folding. I read some articles related to my work and they always show temp (replica_index) graphs for 2-3 replicas , saying that the sufficient sampling had been a

[gmx-users] Add CS ions to system

Hi all, I want to add CS ions to my system by genion but it seems impossible when go through the EM. The molecule section in my top file is: Protein_chain_A 1 Protein_chain_B 1 POPC        238 SOL 20406 NA   681 CL   702 CS   19 The commands t

[gmx-users] proceed from output of MD

Hi, I have run a 20ns MD simulation on my protein structure and about to proceed with Autodock. I am wondering if I have missed anything. The output of the file is gro, so I converted it to a pdb file. Then, when I process it with Autodock Tools, all I get is the water molecules surrounding my pro

R: [gmx-users] metadynamics

Hi, have look to: http://www.plumed-code.org/ and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ www.biomolnmr.org Tel: 0039-0

[gmx-users] charmm in gromacs cut-offs

Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already tested this issue in the latest version, please

[gmx-users] metadynamics

Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

Re: [gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules

On Sat, May 18, 2013 at 10:20 AM, jnsong wrote: > Dear all, > > Recently, I want to add angle_restraints and dihedral_restraints for atoms > in two separate molecules, that is, inter-molecular restraints, not > intra-molecular restraints. > > I add the following into my .top file: > [ angle_restr

Re: [gmx-users] ionic liquids - viscosity via green kubo relation

Krzysztof, You were indeed correct to suggest augmenting the ACF window. For ionic liquids, I have seen ACF windows that are around 500 ps, thank you for your suggestion !!! 2013/5/7 Krzysztof Murzyn > Hello, > > I would try to extend ACF window (10, 50, 200ps) but not too much since you > mi

[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules

Dear all, Recently, I want to add angle_restraints and dihedral_restraints for atoms in two separate molecules, that is, inter-molecular restraints, not intra-molecular restraints. I add the following into my .top file: [ angle_restraints ] ; i jkltype theta0 fc multip