Fwd: [gmx-users] Re: Gromacs error

I have another issue .. I am am preparing the structure for simulation which is a docked complex containing Phospharylated tyrosine. I am using Amber 99 force field and update the residuetypes.dat, aminoacid.rtp, ffbonded.itp files for pTYR but still the error that "Residue 'PTYR' not found in res

[gmx-users] What does it mean by saying mca: base: component_find: unable to open....

Dear gmxers, We have installed gmx-4.5.4 on one cluster from the source, without any errors. I can also run mdrun in non-parallel way successful. However, when I run mdrun in parallel way as follows: mpimdrun -h some messages are given: [node10:03709] mca: base: component_find: unable to o

Re: [gmx-users] Re: Gromacs error

On 06/17/2011 12:18 PM, bharat gupta wrote: thanks.. I fixed the problem by using the command execstack -c filename but I have another issue .. I am am preparing the structure for simulation which is a docked complex containing Phospharylated tyrosine. I am using Amber 99 force field and upd

Re: [gmx-users] Re: Gromacs error

I took all the parameters of Ptyr from amber parameter database and followed what was said in the documentation. Shall mail the changes made for topology On Fri, Jun 17, 2011 at 5:17 PM, Mark Abraham wrote: > On 06/17/2011 12:18 PM, bharat gupta wrote: > >> thanks.. I fixed the problem by using

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Gideon Lapidoth requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Gideon Accept invitation from Gideon Lapidoth http://www.linkedin.com/e/-85v1n9-gp

Re: [gmx-users] What does it mean by saying mca: base: component_find: unable to open....

On 06/17/2011 05:15 PM, xiaowu759 wrote: Dear gmxers, We have installed gmx-4.5.4 on one cluster from the source, without any errors. I can also run mdrun in non-parallel way successful. However, when I run mdrun in parallel way as follows: mpimdrun -h some messages are given: [node10:03709

Re: [gmx-users] Re: Gromacs error

On 06/17/2011 06:36 PM, bharat gupta wrote: I took all the parameters of Ptyr from amber parameter database and followed what was said in the documentation. The fact that you seem to change the capitalization of "PTYR" every time you type it does not inspire confidence that you've taken due ca

Re: [gmx-users] Regarding H-bond autocorrelation

See the Luzar and chandler papers that I believe are mentioned when you run g_hbond -ac. The subtraction is not mentioned in that paper, however. Erik 17 jun 2011 kl. 06.59 skrev bipin singh: > Thanks Sir,for your reply... > I have a silly question regarding the g_hbond's autocorrelation output

[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

Dear GROMACS users, I am trying to construct a cyclic hexa peptide containing all Ala residues. During pdb2gmx conversion using the command(pdb2gmx -ff charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the following error while I am demanding the program to give uncharged termini (

Re: [gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

Thank you for your suggestions. I have checked the topology file with vim, and it looks pefectly, also, the only problem happens when I use genion. One thing that might be possible is that I use the double precision version of gromacs, because when I solve it in water, the written of topology file

[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

For the quick fix: 1. run genion on your topology that does work. Look at this to see the format of the ion atom and residue names 2. Pick a few waters in the structure containing the ligand and replace the OW by the ion and remove the hydrogens, then fix the number of atoms on the second

Re: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

On 18/06/2011 1:13 AM, udaya kiran marelli wrote: Dear GROMACS users, I am trying to construct a cyclic hexa peptide containing all Ala residues. During pdb2gmx conversion using the command(pdb2gmx -ff charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the following error while

Re: [gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

Ye Yang wrote: Thank you for your suggestions. I have checked the topology file with vim, and it looks pefectly, also, the only problem happens when I use genion. One thing that might be possible is that I use the double precision version of gromacs, because when I solve it in water, the wri

Re: [gmx-users] load imbalance

Thanks for the reply. Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that? Thanks, Nihal On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham wrote: > ** > On 17/06/2011 12:44 PM, E. Nihal K

Re: [gmx-users] load imbalance

On 18/06/2011 10:36 AM, E. Nihal Korkmaz wrote: Thanks for the reply. Would that cause any problems in the simulation? No. It says force 154.9%, does that mean it is applying the wrong force? No, it means calculating the forces is taking an amount of time that is significantly different f

Re: [gmx-users] load imbalance

E. Nihal Korkmaz wrote: Thanks for the reply. Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that? It just means that one (or maybe more) processors are doing a whole lot more

[gmx-users] local pressure v4.5 issues

Dear all, I installed the git version of local pressure calculation from http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure The I invoked mdrun mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 This created a file named "localpressure.dat0".