[gmx-users] Water molecule can not be settled

Dear Gromacs users, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx insert-molecules and solvated with gmx solvate. When I tried to run md, I got the following

[gmx-users] simulation of long hydrocarbons

Dear all I want to simulate a decane molecule and I used some of the parameters of a paper. The paper studied only C-C-C-C dihedral parameter. As far As I know, the "CT" show the carbon in the aliphatic hydrocarbons in the OPLS-AA force field. I used the following parameters for decane (for all

[gmx-users] DPD in Groamcs

Dear all is there any possibility of performing dissipative particle dynamics (DPD) in gromacs? Thanks in Advance Praveen -- 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

Re: [gmx-users] Regarding box size and the rlist values

The error tells you exactly what you need to know. Your box size must be twice the cutoff to run (or more likely three times the cutoff to produce useful results). Reducing your cut-off usually means your results don't properly reflect the force field as it was parameterized and should be

[gmx-users] Regarding box size and the rlist values

Hello, I am running a simulation of my system of box length 2.1 nm (since i have less number of molecules and small molecular size), and i am using charmm 36 FF, hence i am using rlist = 1.2 (since these are the parameters for charmm FF in the link