Re: [gmx-users] CHARMM36 force field available for GROMACS

Nice trick - I didn't realise you could chain and group sed regular expressions that way! Neither did I know pdb2gmx had an .arn database. That's two things I've learned... Can I go home now? :-D Mark On Mar 10, 2014 7:32 AM, "Tsjerk Wassenaar" wrote: > cat $pdbfile | sed 's/TIP3/SOL /' | sed

[gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions

Dear Users, I am doing MD simulations involving lysosomal proteins catalases and small organic compounds and would be glad to know how I can achieve this under a pH=5 environment. Thank uou -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] parameters problem

On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ The p

Re: [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions

On 3/10/14, 5:29 AM, MUSYOKA THOMMAS wrote: Dear Users, I am doing MD simulations involving lysosomal proteins catalases and small organic compounds and would be glad to know how I can achieve this under a pH=5 environment. The concept of pH isn't well defined in standard MD. The best you c

Re: [gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions

It depends. Google knows a fair bit about "constant pH md simulation" Mark On Mon, Mar 10, 2014 at 10:29 AM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Dear Users, > I am doing MD simulations involving lysosomal proteins catalases and small > organic compounds and would be glad to

[gmx-users] Spatial distribution

Dear users, I have performed a coarse grain molecular dynamics simulation (MARTINI) to study the association of two identical alpha helix H1 and H2. I would like to analyse the spatial distribution of one helix arround the other and make a 2D representation as in Mark S. P. Sansom, Biochemistry

Re: [gmx-users] Spatial distribution

On 3/10/14, 6:35 AM, Norbert GARNIER wrote: Dear users, I have performed a coarse grain molecular dynamics simulation (MARTINI) to study the association of two identical alpha helix H1 and H2. I would like to analyse the spatial distribution of one helix arround the other and make a 2D represe

Re: [gmx-users] parameters problem

Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote: > > > On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > >> Thank you Mark and Justin. >> Now, I have carried out simulations using PME electrostatic

[gmx-users] Problem in extending simulation with state.cpt while changing number of cores

Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr

Re: [gmx-users] parameters problem

On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information

Re: [gmx-users] Problem in extending simulation with state.cpt while changing number of cores

Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally starte

Re: [gmx-users] parameters problem

To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include "posre.itp" ;#endif ;Include ligand topology #include "ligand.

Re: [gmx-users] parameters problem

Probably you will see that your ligand.itp has an [atomtypes] entry as well as a [molecule] entry, and the former cannot follow any instance of the latter. Such an .itp file must be #included to create the first molecule. You have your protein [molecule] above the #include "ligand.itp" at the momen

Re: [gmx-users] Problem in extending simulation with state.cpt while changing number of cores

Thanks Mark for your reply, I am using gromacs version 4.6.3 with single precision. Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my typing mistake. So the command line was as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr mdrun -s 15ns_new.tpr -o last_15ns.

[gmx-users] about insane.py script on martini website.

I want to generate a .gro file for a coarse-grained model of a single DLPC lipid. I learned I can used the insane.py script on martini website. This is the input command I used: python insane.py -d 1 -x 1 -y 1 -z 3 -l DLPC -asym 1 -sol 0 -o dlpc.gro Yes I get an output but I don't think I have t