Re: [gmx-users] Langevin temperature coupling in Gromacs

Hi, Probably you can, but there is no escaping reading both sets of documentation and following the strategy you learned while doing that. Mark On 19/03/2015 1:32 pm, Kevin C Chan cchan224...@my.cityu.edu.hk wrote: Dear Users, I am thinking whether a Langevin thermostat can be achieved by

Re: [gmx-users] g_dist

On 3/19/15 12:28 AM, RINU KHATTRI wrote: hello everyone i am unable to understand the result of gmx check .it gives frames and time values .g_dist is worked in all protein related residues but i want to calculate the distance between some residues of protein and ligand for ligand i got same

Re: [gmx-users] Tutorial For Installing Gromacs on window

On 3/19/15 12:30 AM, Rajneet kaur Saini wrote: Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation

Re: [gmx-users] pdb2gmx error

Hi, These errors mean exactly what they say. There's a mismatch between your structure file and the residue structure in the database. So you need to look at them both and see what is wrong. Chapter 5 of the manual is your friend. Mark On 19/03/2015 3:17 am, RJ ra...@kaist.ac.kr wrote: Dear

Re: [gmx-users] Mixed Solvent (H2O/CH3CN)

On 3/19/15 8:29 AM, Debashis Sahu wrote: Dear Gromacs users, I have faced a problem recently for the NVT simulation of a small organic receptor in acetonitrile solvent. I got the following errors even varying the box sizes as well as the number of solvent.

[gmx-users] Mixed Solvent (H2O/CH3CN)

Dear Gromacs users, I have faced a problem recently for the NVT simulation of a small organic receptor in acetonitrile solvent. I got the following errors even varying the box sizes as well as the number of solvent. starting mdrun 'Giant Rising Ordinary Mutants for A

[gmx-users] Langevin temperature coupling in Gromacs

Dear Users, I am thinking whether a Langevin thermostat can be achieved by turning on integrator=sd in Gromacs and setting bd-fric. All I want is to make an equivalent mdp file (thermostat part) compared to an NAMD parameter in which the Langevin thermostat is turned on and gamma equals to 5.

[gmx-users] parallel calculation problem in implicit solvent modeling

Dear all, I had a problems with parallel calculation of a implicit solvent problem. My gromacs is compiled with mpi, so technically, I run mdrun_mpi for my simulation. I am calling 12 cpus for my simulation and started 12 treads. When I put a limited rlist in the simulation, say rlist=4, 12

[gmx-users] Potential modification

Dear, I want to incorporate one potential form in gromacs. Can you please tell me how is it possible here or what is the procedure for thatplease suggest me.. Thanks, Tuhin -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to build up a nafion PDB

Dear all, I want to simulate nafion oligomers in explicit water. Is there any tool or any software where I can build a short nafion residue? How consistent will be the bond length/angle parameters with respect to the employed force field? I am quite new in the filed of molecular

[gmx-users] trjconv - pbc centering and fitting

HI everyone, I have crystal structure output from pdb2gmx *eg. aaa.gro* After my 200ns production run , i ran trjconv as below 1. trjconv -n ../index.ndx -f md.xtc -s em.tpr -o md.pbc.xtc -ur rect -boxcenter rect -pbc nojump 2. trjconv -n ../index.ndx -f md.pbc.xtc -s em.tpr -o

[gmx-users] LINCS waring during MD.

Hi all, I am trying to study wetting of water on Graphene oxide(GO). Energy minimization for my gives me following result which, I think is ok. - Step= 5137, Dmax= 1.1e-06 nm, Epot= -9.40777e+03 Fmax= 4.76973e+01,

Re: [gmx-users] using g_energy

Dear Mark Abraham I changed contraint variables and can generate bond energy terms. Thanks for you help!!! Sangeun Jee On Fri, Mar 6, 2015 at 6:18 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No, you've used .mdp settings to convert .itp [bonds] into constraints. Mark On Sat, Mar 7,