Re: [gmx-users] Checkpoint files error

Hi, Use grompp -t state.cpt to do an exact continuation while changing the tpr settings. As you saw, mdrun -cpi expects things to stay the same. The gro file has lower precision, so should be used for visualization convenience only. Mark On Sat, 1 Jul 2017 19:12 Apramita Chand

[gmx-users] Issue with the PDB generated after topology

Dear Gromacs users, I'm running a protein complex simulations with the gromacs software. My complex is two different proteins named chain A (1-166 aa) and chain B (55-131)with 3 ions and one ligand. I have produced the topology for the every component of my complex using pdb2gmx program.

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

Hi Peter, Sorry for the delay. According to your suggestion, I have equilibrated my system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After that, the production step is running successfully. Thanks a lot for your kind help! Best regards, Sudip On Thu, Jun 29, 2017 at 2:32

[gmx-users] Issue with the PDB generated after topology

Dear Mark, Thank you for your reply. My starting pdb sequence on pymol is: A 1-166, B 54-131 After topology generation and solvation, I can display the whole structure with the two chains A and B but in terms of sequence, the chain B is absent. Please, let me know if any further information

[gmx-users] Can not open file: run.trr

Hi everyone, Recently I was run a 30ns gromacs simulation.And for the analysis part, i was copied down the entire file directory of the simulation into an external hard disk and shift it into another computer with same OS and same version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Sure - one should use a tool capable of doing the job, and use its optional capabilities accordingly. Choosing non-bonded exclusions based on bonds, in a way that does not implement the intended model physics, is indeed wrong, but that doesn't make the use of modified 1-4 pair interactions

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, I have now solved the problem. I have added a list of the 1-4 pairs within [ Pairs ] and it has led to the correct equilibrium bond length. Just as reference, information on the forcefield I am using is found in this paper: http://pubs.acs.org/doi/abs/10.1021/cm500365c Cheers, Amanda On

Re: [gmx-users] Issue with the PDB generated after topology

Hi, Your description is unclear - you seem to change whether a protein and a chain are the same thing, or not. So I don't know what you think the problem is :-) Mark On Sun, Jul 2, 2017 at 5:18 PM Khadija Amine wrote: > Dear Gromacs users, > > I'm running a protein

Re: [gmx-users] Can not open file: run.trr

Hi, Use tools like rsync to do your file copies and preserve suitable permissions automatically. And try to avoid copying files > 2GB to partitions formatted in Windows-friendly fashion to e.g. FAT32 file sytems, as external hard drives might be formatted. Mark On Sun, Jul 2, 2017 at 10:59 PM

Re: [gmx-users] Nano-structures equilibration

You have problems with the system and you expect everyone here to be a magician and guess your inputs. What is the forcefield, what is the timestep, how are you describing your graphene sample, what is your number of exclusions for that sample, what is your barostat type during eqilibration?

[gmx-users] Simulation of an acetylated peptide covalently bound to a protein

Hi Gromacs community, I get stuck in a simulation of an acetylated peptide covalently bound to a protein. Could someone please give me some insight? My system consists of a short peptide bound to a protein. The peptide has 4 amino acids, with the N-terminal Val acetylated and the C-terminal Asp

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, On Fri, Jun 30, 2017 at 2:46 AM Alex wrote: > > > > > >> > >> He he, childish :) > > > > David, no offense intended. I just think that when applied to solids, the > entire concept of what works so well for biomolecular systems becomes a bit > of a joke. And vice versa,

[gmx-users] Grid Spacing

Dear All, Which is more appropriate fourier grid spacing for gromos53a6 ff with cutoffs being 0.9 and 1.4nm? 0.16 or 0.12?? I've not seen too many papers with 0.16 being used for this forcefield and that too with cutoffs like 1.0 for rcoulomb and rvdw. Is there any problem if I use fourier

[gmx-users] Multiple output log. xtc .edr files generated using mpirun

Hello GROMACS users, I am trying to run a simulation on a university cluster; I am using gromacs-5.1.2. The problem is while running mdrun, using the following command: mpirun -np 32 gmx mdrun -s prod.tpr -deffnm prod_out -pin on ### I expected gmx mdrun_mpi here but it was not available. I

[gmx-users] Difference between semi isotropic coupling and surface tension option

Dear all Gromacs users I'm simulating a monolayer at water/vacuum interface with Gromacs and I'm studying surface tension and area per lipid variations. the problem that is very confusing me on this subject is that when I use semiisotropic option to impose a negative lateral pressure and so a

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 3

Dear Friends, While performing simulation on our protein of interest, if we want to know the overall charge on our protein then how can we check the same and proceed further for addition of ions to make the system neutral. Regards *Amitabh Jayaswal* *PhD Bioinformatics Scholar* *Banaras Hindu