Re: [gmx-users] question on system blow-up

Hi John, Thank you very much for your reply. After checking my log file, it seems my Metal ion cannot form a stable coordination bonds in simulation. the first 10 missing interactions, except for exclusions: LJ-14 atoms 1180 1572 global 1180 1572 The number 1572 is my

Re: [gmx-users] RAM usage of gmx msd

Hi, thanks a lot for your answer. It contained exactly the information that I needed. Here is a summary of my issue and how I resolved it: Problem: I wanted to calculate lateral diffusion of lipids in a cell membrane using a key atom for each lipid. But gmx msd needs too much RAM.

Re: [gmx-users] SIMD options - detection program issue

Hi, Good to know your system instability issues were resolved. (As a side-note you could have tried to use elrepo which has newer kernels for CentOS.) The SIMD detection should however not be failing; can you please file an issue on redmine.gromacs.org with cmake invocation, CMakeCache.txt and

[gmx-users] Free webinar on accelerating sampling in GROMACS with the AWH method

Hi, Since version 2018, GROMACS supports the Accelerated Weight Histogram method to accelerate sampling along reaction coordinates. With AWH conformational transitions can be accelerated by orders of magnitude. On Tuesday, September 24, from 15:00 we are organizing a free webinar on the AWH

Re: [gmx-users] question on system blow-up

Hi, > Dear gmx-users, > > Could I ask a question on system blow-up? Thanks! > I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found > system blow up at around 1ns. ("atoms involved moved further apart than > the > multi-body cut-off distance") > > When I checked the trajectory

Re: [gmx-users] Tesla GPUs: P40 or P100?

Hi, thanks for your suggestion - we hadn't considered those Quadros, but they do sound like a great option. I'll be asking for availability and pricing. Cheers Matteo Il giorno gio 19 set 2019 alle ore 20:39 Szilárd Páll < pall.szil...@gmail.com> ha scritto: > Hi, > > I strongly recommend the

[gmx-users] Position Restraints MD

Dear all, I am doing MD simulation of protein and metal atom. I had applied position restraints on metal atom. I had applied it as follows- ( kindly correct me if i am wrong) first made an index of metal atom and generated the posre_ion.itp file using gmx genrestr and then added the force and

[gmx-users] question on system blow-up

Dear gmx-users, Could I ask a question on system blow-up? Thanks! I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found system blow up at around 1ns. ("atoms involved moved further apart than the multi-body cut-off distance") When I checked the trajectory files: nvt.trr,