[gmx-users] Temperature and Pressure coupling in NVT.mdp, NPT.mdp and md.mdp

Hello everybody, Can anybody please help me as I am confused between the Temperature and Pressure coupling in the different .mdp files. Can you please tell me what is the difference between the Temperature and Pressure coupling in the NVT.mdp, NPT.mdp during the equilibration and in the md.mdp

Re: [gmx-users] Thin film drifting

On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: > Den 2020-03-29 kl. 19:43, skrev Alex: > > Thanks. > > > > On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < > sp...@xray.bmc.uu.se> > > wrote: > > > >> Den 2020-03-29 kl. 15:16, skrev Alex: > >>> Thank Prof. van der Spoel for the

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in

Re: [gmx-users] Thin film drifting

Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: > Den 2020-03-29 kl. 15:16, skrev Alex: > > Thank Prof. van der Spoel for the response. > > No, it isn't. The thin film is solid. There are interaction within the > thin > > film and with water in the interface. > > > > Please

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water

[gmx-users] geometry optimization of metalloenzyme

Hello everyone, I am trying to minimize the potential energy of a metalloenzyme containing Ni and Fe atoms. What is the best way to constrain (fix?) the position of the active site atoms during the geometry optimization? I have tried introducing bonds with relatively high force constants and

Re: [gmx-users] Thin film drifting

Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water molecules are hidden); It shows minimization,

Re: [gmx-users] replica exchange simulations performance issues.

After much experimentation I managed to run mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 on a single node at 27 ns/day. This scaled up for 73 replicas on my 190 000 atom system ( using the same logic -np num_sims*12) on our gadi cluster in

Re: [gmx-users] replica exchange simulations performance issues.

On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea).

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode