[gmx-users] NPT or NVT

Dear all, I’ve a doubt/question. I ran a long simulation of my system (100ns) at 298K. Now I want to see the effect of the T on my system and I want to run a 20ns simulation at 350K and 400K, now my question is: Do I have to run this simulation under the NPT condition or under the NVT (using an

[gmx-users] position restraints

Hi, I am including position restraints as one of the directives under [moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)). [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd

Re: [gmx-users] how to add parameters to Topolbuild

On Wednesday, January 1, 2014 at 6:33 PM, Tom dna...@gmail.com wrote: Can someone help us about how to add misssing parameters into Topolbuild? We are using topolbuild to build *top file for a molecular which has amide group. Topolbuld reports missing parameters of bonding, angle and

Re: [gmx-users] position restraints

On 1/2/14, 6:41 AM, Chetan Mahajan wrote: Hi, I am including position restraints as one of the directives under [moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)). [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i

[gmx-users] Implicit solvent, Simulated annealing, Remove motion of center of mass

Hi all, The system I'm working with is Protein G (ID: 1PG) with a graphene surface using Implicit Solvent. I perform an energy minimization using steepest descent with 1000 steps and 0.001 ps time step. Then I use simulation annealing for 200ps to heat the system to 300K. After heating, the

[gmx-users] insert the new force field

Hi, Can I insert the other force fiels such as COMPASS to GROMACS? Thanks for anyone's help. Best regards! Zhicheng -- 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