[gmx-users] Topology generation of molecules

If PRODRG is not giving suitable results . Can I use Antechamber output in GROMACS for the topology generation of molecules ?  . Regards,  ___                     ABID  ALI Junior Research Fellow, Lab No.  P-133, Computational Chemistry Unit, Dr

[gmx-users] Minimization error

Dear Gromacs users, I am running simulation of apo  protein. In minimization step when I am running this command    " gmx mdrun -v -deffnm em"  the error appears that " Fatal error: There is no domain decomposition for 24 ranks that is compatible with the given box and a minimum cell size of

[gmx-users] Protein is Jumping from water Box

Dear Gromacs users, I have run 40 ns simulation , after 20 ns simulation my protein is continuously jumping from water Box. Is there any periodic boundary conditions issue with my system or an other error is that . Kindly give your valuable remarks. Thanks, Regards,  Abid Ali Channa, Junior

[gmx-users] Rmsd Problem

Deaer Gromacs users, I have a problem in analyzing my MD simulation results of RMSD the graph of apo protein lies below while the graph lines of ligand bound complexes lies above.I am not getting what this graph is showing. Kindly give me some clues to interpret this graph. Here I am attaching

[gmx-users] Distance between two specific residues

Dear Gromacs users, I am trying to calculate distance between two specific residues of active site of my protein in MD. I have made separate .index file of  two specific groups. Then I am trying this command " gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu

[gmx-users] Distance between two specific residues

Dear Gromacs users, I am trying to calculate distance between two specific residues of active site of my protein in MD. I have made separate .index file of  two specific groups. Then I am trying this command " gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu

[gmx-users] Acpype topolgy error

Dear Gromacs users, I am going to run complex simulation. I have prepared ligand topology through acpype , from where I have taken two files .gro and .itp file. I have used Gromos ff for my simulation . I got atom type error while running this command  " gmx grompp -f em.mdp -c solv.gro -p

[gmx-users] How I merge all .tpr files

Dear Gromacs users, I have run 50 ns simulation job in five steps. Now I am going to analyze  energy, rmsd, rmsf etc of these simulations. I have merged all files like .gro, .xtc, .edr etc. But I want to merge all extend tpr files in one file for analyzing purpose. Is there any command to merge

[gmx-users] Equilibration error

Hi gromacs users, I have found error in equalibration step  in my simulation. Kindly give your valuable suggestions. Fatal error: 2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually

[gmx-users] Extending job error

Hi gromacs users, I am running 50 ns seconds MD  job in 5 differents parts like wise 10, 10 ns. How can I set enviroment or command through which I can run in single command. I have used gmx convert-tpr command but it requires extend command after every 10 ns time. Is there any option in

[gmx-users] Topology error

Dear gromacs users, I am working on protein-ligand simulation, I have prepared ligand topology through PRODRG server, it is generating many files , I am taking co-ordinate file Gromos-87/Gromacs (polar/aromatic hydrogens) and gromacs topoplogy file interms drg.itp, problem is that PRODRG only

[gmx-users] How I extend command

Hi gromacs users, I am working membrane complex simulation of 20 ns, 100, steps , my simulation is reached 40,0 steps it stoped by mistakenly , How I can extend this 40 lac steps to 1 crore steps rather than starting , thanks in advance Abid Ali Channa, Junior Research Fellow, Lab

[gmx-users] How I extend command?

Hi gromacs users, I am working membrane complex simulation of 20 ns, 100, steps , my simulation is reached 40,0 steps it stoped by mistakenly , How I can extend this 40 lac steps to 1 crore steps rather than starting , thanks in advance Abid Ali Channa, Junior Research Fellow, Lab

Re: [gmx-users] gromacs

want to use. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Abid Channa [abid.cha...@hotmail.com] Sent: Friday, February 13, 2015 5:56 PM To: gromacs.org_gmx-users

[gmx-users] gromacs

Hi gromacs users, I am working on Sotase A complex simulation, I have done 5 ns simulation, I want to extend simulatiom from 5 to 10 ns, is there any person tell me extending command quickly? Thanks in advance for Justin Lemkul Abid Ali Channa, Junior Research Fellow, Lab No. P-133,

Re: [gmx-users] gromacs

new steps should give you an additional 5 ns if your timestep is 2 ps). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Abid Channa abid.cha...@hotmail.com Sent: 12 February

[gmx-users] send this as a post

Thanks,, Regards,, Abid Ali Channa,Junior Research Fellow, Lab No.  P-133, Computational Chemistry Unit,Dr .Panjwani Center for Molecular Medicine and Drug Research,International Center for Chemical and Biological Sciences,University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74

hi gromacs users i got error in step four in protein-ligand complex how can i fix it: Fatal error: number of coordinates in coordinate file (solv.gro, 36526)             does not match topology (topol.top, 365267) when i want to ran this: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr