[gmx-users] Query on generate velocities and gen_temp in mdp files for REMD simulations

Dear Help, I am trying to run REMD simulations and found couple of interesting discussions on GROMACS mailing list regarding ensembles which can be used during REMD. I will be running REMD of small peptide in explicit solvent and I am confused about gen_temp and gen_vel parameters for these simul

[gmx-users] xpm2ps issue

Dear Gromacs Users and Developers, I am doing do_dssp analyses using a trajectory and structure file both in pdb format. My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps doesn't show ticks on X-axis. I get following message: Auto-tick spacing failed for X-axis, guessing

[gmx-users] xpm2ps

Hi Gromacs mailing list supporters, I had previously posted query on xpm2ps. http://lists.gromacs.org/pipermail/gmx-users/2013-April/080729.html There are 100 frames in the simulations. I tried fiddling with the parameters in the .m2p file such as matrix spacing and X-axis minimum and maximum

[gmx-users] virtual sites in gromacs

Dear Users, I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am using following command. pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh Upon visualisation I could see triangle like sites. Does the output seem right? 75 1VALMN11 2.913 3.551 3.288

[gmx-users] virtual sites

Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbohydrate. Is it possible to apply virtual sit

[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs

preferred for polar solutes (drugs) like sugars. What is the reference for these values for polar solutes i.e. sugars.? I would appreciate if there is any example of such calculation done in gromacs. Many thanks, Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO

[gmx-users] Re: Drug-Enzyme tutorial- LIE energies in gromacs

wondering if there are reports where LIE has been parameterise using PME and PBC. Thanks and Regards, Neha 2009/3/24 Neha Gandhi > Dear GMX-users, > > In the Gromacs Drug/Enzyme complex solvation tutorial by John E. Kerrigan , > in the end they mention about the LIE calculation. The g

[gmx-users] drug-enzyme simulation.

5ns gives issues. 2) I ran another similar but smaller system and the complex is stable even after 8ns. What went wrong with the simulations in case 1? Is there a way to fix this problem? Your help is much appreciated. Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of

Re: [gmx-users] drug-enzyme simulation.

Many thanks Justin, It worked! 2009/3/29 Justin A. Lemkul : > > > Neha Gandhi wrote: >> >> Hi List, >> >> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated >> annealing followed by  production runs of 5ns usng NPT and PBC and >> PME

[gmx-users] GROMOS carbohydrate forcefield 45a4

emperature? What parameters are important to validate ff for such molecules? Your help is appreciated. -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 ___ gmx-users mailing l

[gmx-users] genion

Hi List, I was just wondering what is the relationship between the molarity and the number of molecules. I have a system with 20 atoms of ligand, 761 water molecules, the box volume of 2.86 nanometer cube. I added 0.5 M NaCl salt concentration using genion. I need to add. Genion put 7 Na+ and 7 Cl