[gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M

Hello dear users, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found (

[gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M

Hello, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found (

[gmx-users] The sum of the two largest charge group radii (32.555389) is larger than rlist

Hello, I am trying to switch my simulations from using Verlet cutoff scheme to Group. To do this I replace "cutoff-scheme = Verlet" with "cutoff-scheme = Group" and "rlist = 1.2" with "rlist = 1.4". As a result GROMACS gives me the following warning when I try to generate the tpr file with

[gmx-users] Using custom potential for electrostatics between protein and water

rom: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram > Davtyan <davtyan.a...@gmail.com> > Sent: 06 December 2017 13:57:17 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Usi

Re: [gmx-users] Using custom potential for electrostatics between protein and water

rk suggested you have to replace "cutoff-scheme=verlet" to > "cutoff-scheme=group". > > > Srinivasa > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> o

Re: [gmx-users] Using custom potential for electrostatics between protein and water

you that, sorry. > > Mark > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > wrote: > > > Hello, > > > > I am trying to use a custom electrostatic potential between protein and > > water, with protein-protein and water-water potentia

[gmx-users] Using custom potential for electrostatics between protein and water

Hello, I am trying to use a custom electrostatic potential between protein and water, with protein-protein and water-water potentials remaining the same. I tried running the simulation with the following input script: define = -DPOSRES ; position restrain for protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

eature correctly. Whether it is useful in a study > design is another matter :-) > > Mark > > On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan <davtyan.a...@gmail.com> > wrote: > > > Hi Mark, > > > > I am not sure I understood. If I for example say "energy

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

p exclusions to get this > working, but of course all of those states are sampling unphysical things > from a broken forcefield. That can be OK, but you will have to be able to > defend that claim. > > Mark > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.a...@gm

[gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hello, I am running simulations of two protein domains in tip4p water and 0.15M salt concentration that contain up to 650,000 atoms total. The protein domains are separated from each other at the start of each simulation and I am measuring how the distance between them changes over time. Now, I