[gmx-users] How to port the parmbsc0 correction to gromacs?

Dear GMX users, As parmbsc0 force field significantly improve the representation of alpha/gamma torsions in nucleic acid simulations,i thus want to use the combination of parm99sb+parmbsc0 in Gromacs that was frequently employed in recent publications. However, when i searched the whole forum

Re: [gmx-users] Poor exchange probability for REMD

REMD > To: "Discussion list for GROMACS users" > Date: Saturday, November 19, 2011, 12:14 AM > On 18/11/2011 12:43 PM, ÏéÇ« ¿× > wrote: > > Dear GMX users， > >     Recently i am performing the > REMD simulation with Gromacs program and the temperature > distributi

[gmx-users] Poor exchange probability for REMD

Dear GMX users， Recently i am performing the REMD simulation with Gromacs program and the temperature distribution for each replica was predicted with the server "http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation with 64 replicas , i checked the exchange probabili

Re: [gmx-users] The equilibrium before REMD simulations

Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] The equilibrium before REMD simulations > To: "Discussion list for GROMACS users" > Date: Monday, November 14, 2011, 11:53 PM > On 15/11/2011 2:50 AM, ÏéÇ« ¿× > wrote: > > Dear Justin, > >    Th

Re: [gmx-users] The equilibrium before REMD simulations

greatly appreciated! Best regards! Xiangqian Kong --- On Mon, 11/14/11, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users] The equilibrium before REMD simulations > To: "Discussion list for GROMACS users" > Date: Monday, November 14, 2011

[gmx-users] The equilibrium before REMD simulations

Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of t

Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

07/2011 1:41 AM, Justin A. > Lemkul wrote: > > > > > > ÏéÇ« ¿× wrote: > >> Dear Gromacs Users, > >>   When I use the pdb2gmx command on > my protein-DNA complex, for the A chain which consists of > the protein.pdb2gmx told me as follows: > >>

[gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

Dear Gromacs Users, When I use the pdb2gmx command on my protein-DNA complex, for the A chain which consists of the protein.pdb2gmx told me as follows: Processing chain 1 'A' (1222 atoms, 151 residues) There are 243 donors and 215 acceptors There are 285 hydrogen bonds Will use HISE for residue