Re: [gmx-users] regarding simulation of peptide and protein complex

Hi Rashi To me, it seems more reasonable to use "pdb2gmx" for every molecule that is supported by this utility (i.e. included in a rtp file) as it will be more likely to be FF-compliant (at least for the default rtp files) and thus compatible with your protein. PROD

Re: [gmx-users] Residence time and trjorder

Hi gmx-users, I tried installing the tool, g_residence.c I am using gromacs-4.0.7 I copied it to the src/tools. There, I executed make command # make g_residence cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib g

[gmx-users] Regarding phenyl rings absolutely flat.

Hello Dear, I am using gromacs 4.5.3 version. I am doing simulation of Protein-Ligand complex. My all system is right but I have confusion related to Planarity aromatic ring. My ligand have 3 aromatics ring. I have generated .itp file from Prodrg and i have setup very well. My ligand planer/

Re: [gmx-users] maintained an Hbond using a distance restraint

On 14/07/2011 11:28 AM, Itamar Kass wrote: Hi, I wish to force my system to maintained an Hbond during a simulation. In order to do so I am using a distance restraint protocol, with the following parameters: In the topology file/: /[ distance_restraints ] ; ai aj type index type' low up

Re: [gmx-users] Regarding phenyl rings absolutely flat.

On 14/07/2011 5:50 PM, HARESH AJANI wrote: Hello Dear, I am using gromacs 4.5.3 version. I am doing simulation of Protein-Ligand complex. My all system is right but I have confusion related to Planarity aromatic ring. My ligand have 3 aromatics ring. I have generated .itp file from Prodrg and i

[gmx-users] Force components on ATOM XX

Dear Gromacs Users, Is it possible to get the forces (components, x,y, z) acting on each atom from the simulation  or from the rerun. I need them to calculate the Hessian Similar to http://www.sciencedirect.com/science/article/pii/S0006349507715989 Best, nahren -- gmx-users mailing list

Re: [gmx-users] REMD with 'bad contacts' error

Hi, I had been trying different thermostats, barostats, time steps and coupling times to get remd for the peptide lipid system working and I had even equilibrated each replica for 50 ns before submitting them to remd. However none of them work when I use one processor per replica. That is, I have 5

[gmx-users] XTC I/O error in replica exchange

Hi, I am running a replica exchange simulation using 64 replicas ( using gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors). But, what happens is that after running for a day or so, the simulation crashes with error like 'XTC error, may be you are out of quota'. But,

Re: [gmx-users] Force components on ATOM XX

On 14/07/2011 9:31 PM, nahren manuel wrote: Dear Gromacs Users, Is it possible to get the forces (components, x,y, z) acting on each atom from the simulation or from the rerun. Sure. Check out nstfout in chapter 7 of the manual, and g_traj -h. Mark I need them to calculate the Hessian Simi

Re: [gmx-users] REMD with 'bad contacts' error

On 15/07/2011 12:40 AM, Sheeba Jem wrote: Hi, I had been trying different thermostats, barostats, time steps and coupling times to get remd for the peptide lipid system working and I had even equilibrated each replica for 50 ns before submitting them to remd. However none of them work when I

Re: [gmx-users] XTC I/O error in replica exchange

On 15/07/2011 3:06 AM, Sanku M wrote: Hi, I am running a replica exchange simulation using 64 replicas ( using gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors). But, what happens is that after running for a day or so, the simulation crashes with error like 'XTC er

Re: [gmx-users] XTC I/O error in replica exchange

Hi Sanku, How large is your XTC file? This error also shows up when the XTC file grows too large for the filesystem it's on (frequently 16 GB for ext3 filesystems on Linux, for example). MZ On Thu, Jul 14, 2011 at 1:06 PM, Sanku M wrote: > Hi, >   I am running a replica exchange simulation usi

[gmx-users] Weird problem

Hello All, I am having a weird problem and I do not know whether it has to do anything with Gromacs or the cluster setting I am using. When I run a MD simulation (on any protein), the job automatically terminates overnight without an error message. I mean if I start the job early in the morning it

Re: [gmx-users] Weird problem

Sayan Bagchi wrote: Hello All, I am having a weird problem and I do not know whether it has to do anything with Gromacs or the cluster setting I am using. When I run a MD simulation (on any protein), the job automatically terminates overnight without an error message. I mean if I start the jo

[gmx-users] Replicate Triclinic Bilayer

I would like to replicate the tilted DPPC gel phase from Marrink's website laterally, so that I have 4 times the area. But since the coupling is anisotropic, there are 9 box dimensions, and the triclinic geometry confuses me. I have seen that you can use editconf and -translate, followed by mergin

Re: [gmx-users] Replicate Triclinic Bilayer

Max Watson wrote: I would like to replicate the tilted DPPC gel phase from Marrink's website laterally, so that I have 4 times the area. But since the coupling is anisotropic, there are 9 box dimensions, and the triclinic geometry confuses me. I have seen that you can use editconf and -tran

[gmx-users] g_dist with multiple chains of molecules

Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, I want to calculate

Re: [gmx-users] g_dist with multiple chains of molecules

Sanku M wrote: Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain,

[gmx-users] malloc on mac

Hi all, I am trying to find all possible h-bonds between chains in my complex. I am using: g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num system_run1_MD050_fitbb_Hbnum_all.xvg -hbn system_run1_MD050_fitbb.xtc_Hbond_a

Re: [gmx-users] g_dist with multiple chains of molecules

On 15/07/2011 6:37 AM, Sanku M wrote: Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of

Re: [gmx-users] malloc on mac

On 15/07/2011 11:48 AM, Itamar Kass wrote: Hi all, I am trying to find all possible h-bonds between chains in my complex. I am using: g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num system_run1_MD050_fitbb_Hbnum_all.x

[gmx-users] monte carlo simulation in gromacs

Dear all, I wanted to do perform a Monte carlo simulation of RNA using coarse grained force filedn in gromacs.when i do pdb2gmx i dont get option for Coarse grained ff.is mC integrator availble in gromacs? thanks in advance, sree. -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] monte carlo simulation in gromacs

On 15/07/2011 1:25 PM, sreelakshmi ramesh wrote: Dear all, I wanted to do perform a Monte carlo simulation of RNA using coarse grained force filedn in gromacs.when i do pdb2gmx i dont get option for Coarse grained ff.is mC integrator availble in gromacs? GROMA