[gmx-users] Reference file for harmonic restraints

Hi all, I'm running several sequential minimizations and MD simulations with gromacs after translation of part of my system (the rest being harmonically restrained) and I'm looking for a way to specify unique reference coordinates for all simulations The way I understand Gromacs, you define a

[gmx-users] Mutation on membrane protein - Charmm36 for Gromacs

Hello Gromacs users I'd like to use Gromacs to find free energy change in a membrane protein upon single-residue mutation Does anyone have proper forcefield files for doing this ? LIke Charmm36_AA_MUTATION_FORCEFIELD for mutated proteins mixed with charmm36.ff_4.5.7 for lipids ? (I've

[gmx-users] Can somebody explain how to set (XY) hexagonal symmetry pbc in gromacs ?

Hello Gromacs users Going from Charmm to Gromacs, I'm trying to simulate a membrane protein inserted into a membrane : I already got the gro and topol file for gromacs for my entire system : Prot + lipids + Water - minimization in rectangular pbc also works fine Now I'm stuck on how to tell

[gmx-users] Post-analysis of residue residue interactions

Dear gromacs users We've run umbrella sampling simulations (with pull) of proteinA/ProteinB dimer turning into two separate monomers We have 25 simulation windows each of 10 ns MD (1000 frames) and proteins containing 132 residues We now want to calculate interaction energy (VDW Elec) between

Re: [gmx-users] Post-analysis of residue residue interactions

On Thu, Feb 2, 2017 at 2:41 PM CROUZY Serge 119222 <serge.cro...@cea.fr> wrote: > > Dear gromacs users > > We've run umbrella sampling simulations (with pull) of > proteinA/ProteinB dimer turning into two separate monomers We have 25 > simulation windows each of 10 ns MD (1

[gmx-users] Significance of abscissa in pmf from 2 reactions coordinates

Dear Gromacs users I'm running pull simulations using two reaction coordinates 1) distance between c.o.m. of G1 and G2 (G1 and G2 groups of atoms) 2) distance between c.o.m. of G3 and G2 same pulling force (umbrella potential), 25 windows At the end of the treatment by g_wham I can have 3

[gmx-users] Pull group coordinates not expected in pullx files

Dear Gromacs users I'm running umbrella sampling simulations using 2 reaction coordinates: 1 between protein chain A and protein chains BC and the other between chain D and same chains BC (harmonically restrained with DPOSRES) Restraints along X only with 500 kj/mol force Things run OK but when

[gmx-users] Free energy profiles with Pull code : dimer/dimer interactions

Dear gromacs users In previous mail on the list Justin argued about free energy calculations with Pull code that: "For general protein-ligand complexes, it is *NOT* appropriate to assume one-dimensional pulling or applying position restraints to the protein. Our paper (from which the tutorial

[gmx-users] Can't find alchemical-gromacs.py

Dear gromacs users I'm following the alchemistry.org gromacs4.6 example on ethanol solvation free energy I've run the simulations and I'm now at the stage of the analysis I installed pymbar.git and pymbar-examples.git But in the alchemical-free-energy directory I find alchemical_analysis.py but

Re: [gmx-users] Adding FE2+ or FE3+ into the system

I'm interested as well in knowing how to get decent parameters for Fe2+ >From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp We have Zn2+ (What is a reference for these parameters ?) name bondtype mass charge ptype CA ;name at.num mass charge ptype

Re: [gmx-users] Adding FE2+ parameters

Serge 119222 <serge.cro...@cea.fr> wrote: > I'm interested as well in knowing how to get decent parameters for > Fe2+ > > From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp > We have Zn2+ (What is a reference for these parameters ?) > > name bondtype

[gmx-users] where do Zinc parameters come from ?

Hello users Can anyone tell me where the LJ parameters for Zn2+ come from in the Gromacs gromos54a7.ff force field ? (Literature reference for instance) ;name at.num mass charge ptype c6 c12 ZN2+ 30 0.000 0.000 A 0.0004182025 9.4400656e-09 I'm

Re: [gmx-users] Distance between centers of mass

Hi Justin Bouncing back on your early answer about gmx distance, I noticed something strange (to me) I'musing the same instruction for a protein file prot.gro gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" and now I'm running umbrella sampling with pull code

[gmx-users] Strange pullx coordinates (PMF calculations)

Dear gromacs users I've been running gromacs for several years, and enjoyed it.. I've been running PMF calculations for protein DNA interactions without problems until recently: Now I'm puzzled with the X coordinates being written in the pullx files (and thus taken as reaction coordinate values

[gmx-users] 3. Re: Strange pullx coordinates (PMF calculations) (Justin Lemkul)

... This does not make sense ... Thanks a lot On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote: > Dear gromacs users > > I've been running gromacs for several years, and enjoyed it.. > I've been running PMF calculations for protein DNA interactions without > problems until rece

[gmx-users] 5. Re: 3. Re: Strange pullx coordinates (PMF calculations)

each line of the pullx files ... This does not make sense ... Thanks a lot On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote: > Dear gromacs users > > I've been running gromacs for several years, and enjoyed it.. > I've been running PMF calculations for protein DNA interactions without >

[gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF

of these tpr in g_wham calculations? Thanks a lot On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote: > Hello Justin- > In MY pullx first column is Time and second column is absolute > coordinate of the COM of the pulled group Maybe we are missing an option > which would print X and dX in the

[gmx-users] Restart dynamics when trr files removed

Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)... But NO -

Re: [gmx-users] Restart dynamics when trr files removed

Re: ligand in water (Bratin Kumar Das) 3. Re: water mediated Hbond (Bratin Kumar Das) 4. nmr distance restraints (Eiso AB) 5. Restart dynamics when trr files removed (CROUZY Serge 119222) 6. Re: Restart dynamics when trr files rem

[gmx-users] Problem restarting job 2016.4 with gromacs 2019-4

Dear Gromacs users We just installed Gromacs 2019.4 And I get an error restarting free energy jobs (pull) run with Gromacs 2016.4 I' m using one GPU gmx mdrun -nt 20 -s umbrella3_60ns.tpr -cpi umbrella3.cpt -deffnm umbrella3 -pf pullf-umbrella3.xvg -px pullx-umbrella3.xvg GROMACS version: