[gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

Hello All, Presently we are working in generating dihedral drivers for AIB dipeptide in gromacs. We would like to create energy contour maps for different phi, psi angle for AIB in gromacs. We are unable to create the correct energy map vs phi/psi angle of AIB dipeptide during energy minimization

Re: [gmx-users] Error in free energy calculation

Thank you everyone for your reply. I have resolved the problem for reply of Justin from previous mail at gmx list. Thank you Justin again On Thu, Mar 16, 2017 at 5:57 PM, Amir Zeb wrote: > You probably follow umbrella sampling for free energy calculation. > If it is so,

[gmx-users] Calcium ions in GMXPBSA approch

Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation. I have two question, please guide me:1- must I remove calcium ions in free energy calculation?2- If I remove calcium ions, 

Re: [gmx-users] Performance advice for newest Pascal architecture

Hi, I'd recommend the Quadro P6000 or Tesla P40. These are the large chips equivalent with the TITAN X Pascal with high single precision throughput, slightly faster than the P100. The P5000 is not bad, but it's slower. It has a chip similar to the 1080 (not sure about the clocks, those might be

Re: [gmx-users] converting with trjconv

Dear Mark, Thank you, it works with cpptraj. Best regards, Oleksii -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] converting with trjconv

Hi, Not with a GROMACS tool. I would look at the cpptraj or mdanalysis packages to handle such conversion. Mark On Thu, 16 Mar 2017 13:53 Oleksii Zdorevskyi wrote: > Dear Gromacs users community, > > I need to convert Gromacs trajectory file(.gro) to Amber

[gmx-users] converting with trjconv

Dear Gromacs users community, I need to convert Gromacs trajectory file(.gro) to Amber format(.trj). When I use trjconv in the folloving way: gmx trjconv -f dodecamer.gro -o dodecamer.trj I get an output file dodecamer.trj.xtc, i.e. it is in .xtc format. Is it possible to obtain a trajectory

Re: [gmx-users] Error in free energy calculation

You probably follow umbrella sampling for free energy calculation. If it is so, you may change the position of your drug.itp file in topology file, means that before the protein topology. I hope this might solve your problem. Good luck! Amir On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar

Re: [gmx-users] Lipid head movement normal to monolayer.

Thanks Catarina. On 16 Mar 2017 10:53 a.m., "Catarina A. Carvalheda dos Santos" < c.a.c.dossan...@dundee.ac.uk> wrote: > Hey, > > I'm not sure about lipid headgroups "emersing" "into water". Maybe > calculate the average and individual positions of the P and/or N atoms in > the z axis for each

Re: [gmx-users] Peptide orientation in lipid bilayers

On 3/16/17 2:11 AM, Sanket Ghawali wrote: Dear, gmx-user, Hello everyone, I am simulating a peptide in POPC:POPG lipid bilayer. Currently following the Tutorial 2: KALP15 in DPPC, I would like too know how to initially place the peptide 30 A away and parallel to one side of the lipid

Re: [gmx-users] Error in free energy calculation

On 3/16/17 5:49 AM, Tasneem Kausar wrote: Dear All I am trying to perform free energy calculations of a protein drug system. I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug molecule is defined in separate drug.itp file. From the discussions of mailing list I have

Re: [gmx-users] Error in free energy calculation

As article name in reference says PLUMED can be used for free-energy calculations with molecular dynamics. On Thursday, March 16, 2017 1:23 PM, Hannes Loeffler wrote: On Thu, 16 Mar 2017 10:09:58 + Vytautas Rakeviius wrote: >

Re: [gmx-users] LINEAR INTERACTION ENERGY

You need separate energygrps (http://manual.gromacs.org/online/mdp_opt.html (output control) for all average components in LIE equation: Protein, Ligand and solvent.Probably you will need "gmx energy" too to extract average Ligand-solvent interaction terms from edr file before inserting them

Re: [gmx-users] LINEAR INTERACTION ENERGY

Thanks. You have mentioned "proper energy groups" in mdp file Could you please say more about it? Thanks, Kulkarni.R From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Vytautas

Re: [gmx-users] Error in free energy calculation

On Thu, 16 Mar 2017 10:09:58 + Vytautas Rakeviius wrote: > You should try to add PLUMED (plumed.org) to GROMACS for such > things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, > D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable > plugin

Re: [gmx-users] Error in free energy calculation

I can't help you much because I have not really paid attention how restraints in alchemical free energy simulations are handled in newer versions of Gromacs. I understand that [intermolecular_interactions] is a new section that allows using restraints based on global indices. The error message

Re: [gmx-users] Lipid head movement normal to monolayer.

Hey, I'm not sure about lipid headgroups "emersing" "into water". Maybe calculate the average and individual positions of the P and/or N atoms in the z axis for each frame. It's normal that there are some fluctuations though. Anyways, if you want to compare the movement of each lipid molecule in

Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in protein. You must set proper energygrps in mdp file so you get 2 edr files from runs and in the end you use "gmx lie" (http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between those two edr

[gmx-users] LINEAR INTERACTION ENERGY

Hi gromacs users, In order to calculate delta G (Gibbs free energy) for protein ligand binding, what are the steps to be followed in Linear interaction energy? Are there any tutorials for the same? Thanks, Kulkarni.R -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Error in free energy calculation

You should try to add PLUMED (plumed.org) to GROMACS for such things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications,

Re: [gmx-users] COMMAND TO DISPLAY SIMULATION COMPLETION TIME

Thanks From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nikhil Maroli Sent: Thursday, March 16, 2017 7:41 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re:

[gmx-users] Error in free energy calculation

Dear All I am trying to perform free energy calculations of a protein drug system. I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug molecule is defined in separate drug.itp file. From the discussions of mailing list I have found that this is not a problem. To obtain the

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

I altered distance restraints according to your comment into: [ distance_restraints ]  195 281 1 1 1 0.4 0.44 0.48 1000Still get same issue that 195 and 281 even move away from each other. Here link to all files again, hopefully it will not be distorted.

Re: [gmx-users] COMMAND TO DISPLAY SIMULATION COMPLETION TIME

gmx mdrun -v -v is the flag to use for the above -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Peptide orientation in lipid bilayers

Dear, gmx-user, Hello everyone, I am simulating a peptide in POPC:POPG lipid bilayer. Currently following the Tutorial 2: KALP15 in DPPC, I would like too know how to initially place the peptide 30 A away and parallel to one side of the lipid bilayer. Any suggestions on how to go about doing