[gmx-users] Meaning of n-n hydrogen bond

Dear gmx users, Upon using g-hbond with the -hx option, to calculate hydrogen bonds in the mainchain, we are supposed to get a list of all n-n+1 hydrogen bonds, with i = 0 - 6. But, I am regularly getting several n-n hydrogen bonds. What is the meaning of a hydrogen bond of a residue with itself

[gmx-users] Can we compare results from versions 3.2 & 3.3.1

Dear Users, I have simulation data collected using Gromacs version 3.2 . As it was allowed in that version, I have used r_list = 1.1, r_coulomb = 1.0, r_vdw = 1.0, with PME coulomb type and switch for vdw type , while collecting the data. Now, I am running another simulation using the recent 3.3

[gmx-users] eneconv error

Dear users, I am getting extra frames upon concatenating my edr files. I am using a time step of 0.5 ps . Each edr file , of 2 ns, has exactly 4000 frames, but upon concatenating files of total of 10 ns, I am getting 20004 frames. But, my xtc files upon concatenation give me the required number o

[gmx-users] compressibility value for SPC water

Dear all, I read from the mailing list archives, that it is not just the value of tau_p but the ratio of compressibility to tau_p which matters in Berendsen presure coupling. I am using SPC water as the solvent. Is there any ideal value for compressibility to be used for SPC water? i have used a

[gmx-users] Error during mdrun

Thanks, Tsjerk and Mark. Here's what the end of my log file says : Step Time Lambda 524390010487.800780.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.019872 61 62 0.004609 After LINCS

[gmx-users] Error during mdrun

Dear all, At times during the md run of my peptide, the run crashes and I get the following error displayed - "Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates MPI process rank 0 (n0, p3089) caught a SIGSEGV. MPI process rank 1 (n0, p3090

[gmx-users] Re : tau_p

Thank you, Sir. I read from the mailing list archives, that it is not just the value of tau_p but the ratio of compressibility to tau_p which matters in Berendsen presure coupling. I am using SPC water as the solvent. Is there any ideal value for compressibility to be used for SPC water? i have u

[gmx-users] PMF calculation

Dear all, I am working on a tripeptide and would like to calculate Potential Mean Force for the tripeptide. Suggestions to calculate PMF are awaited. Regards, Chetana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

[gmx-users] tau_p

Dear all, I am running md simulations on a decapeptide, using pressure coupling [npt]. My box is octahedral and box dimensions are set at peptide length plus twice the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the average pressure had come down to 2.6 bar, though fluctuat