[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU)

Dear All I am trying to run the free-energy simulation using TI method in gromacs 2019.1 in a GPU machine (containing two Nvidia Geforce 1080 TI cards ). But unfortunately, am unable to run the free-energy simulation run on GPU. The normal MD simulation (without free-energy )is able to run perfe

Re: [gmx-users] Steps for Markov State Modelling

On 3/14/19 4:31 PM, Dallas Warren wrote: https://www.google.com/search?hl=&site=&q=MSM+analysis+%20Frank+Noe Also relevant: https://www.livecomsjournal.org/article/5965-introduction-to-markov-state-modeling-with-the-pyemma-software-article-v1-0 -Justin Catch ya, Dr. Dallas Warren Drug D

Re: [gmx-users] Steps for Markov State Modelling

https://www.google.com/search?hl=&site=&q=MSM+analysis+%20Frank+Noe Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - Wh

[gmx-users] Steps for Markov State Modelling

Dear all, I have a protein trajectory in xtc format. I want to do the MSM analysis on this trajectory to see how the process is going on and the meta-stable states. I have followed the Video series by Frank Noe and team on MSM, but it is not clear to me how to start it. I have some questions

Re: [gmx-users] PDB file that can be read in Gromacs

Hi. First request, try to go through gromacs documentation and tutorials. You will get the clue. Topology of any nonprotein should be generated by a third party software or scripts depending on the forcefield. Have a detailed look into the tutorials. That will definitely help you. Thank you On

Re: [gmx-users] PDB file that can be read in Gromacs

On 3/14/19 3:21 PM, Phuong Chau wrote: Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed t

[gmx-users] PDB file that can be read in Gromacs

Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed the error of "Residue 'UNL' not found in resi

Re: [gmx-users] Simulation is very slow

Dear Yeongkyu, In what sense is it slow? What are you comparing to and for what input data? Are you using both GPUs or only 1 at a time? Do you have any idea of relative performance differences for each of the GPUs you have? A recent inquiry on the list wanted a comparison between the two GPU

Re: [gmx-users] Simulation is very slow

Did you remember to use the -DGMX_GPU =ON CMake option when you built the new version? Mike Moir -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of ??? Sent: Thursday, March 14, 2019 8:56 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [**

Re: [gmx-users] Simulation is very slow

Hi, We can't help without more information. Have you checked the log file to make sure the GPUs are being seen/used? Can you post a link to a sample log file? Kevin On Thu, Mar 14, 2019 at 11:57 AM 이영규 wrote: > Dear gromacs users, > > I installed gromacs 2019 today. When I run gromacs, it is r

[gmx-users] Simulation is very slow

Dear gromacs users, I installed gromacs 2019 today. When I run gromacs, it is really slow. I don't know the reason. I am using GTX 1080 TI and TITAN XP for GPU and I have 8 cores. Please help me. Sincerely -- Yeongkyu Lee M.S student Department of Physics 501, Jinjudaero, Jinju, Gyeongnam <

Re: [gmx-users] User tabulated potential and VdW Modifier

Hello everybody, I sent a message a week back with the same title and I hope this gets put into the right thread now (did not know how to respond directly). I actually did some more testing and I think I found out how everything works and I'm going to leave this here in case someone else ever w

[gmx-users] Dielectric constant

Dear gromacs users,How can I calculate dielectric constant of a polymer in gromacs?Thanks in advance. -- 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 http://www.gromacs.org/Support/Mail

[gmx-users] WG: WG: Issue with CUDA and gromacs

Dear all, I was not sure if the email before reached you, but again many thanks for your reply Szilárd. As written below we are still facing a problem with the performance of your workstation. I wrote before because of the error message when keeping occurring for mdrun simulation: Assertion f

Re: [gmx-users] gromacs performance

Dear Mr Szilárd Páll Give me advice please. I'm going to purchase a videocard for MD. But I doubt the choice between one RTX 2080 Ti and two GTX 1070 Ti. What will be better?  Thank you for advance >Среда, 13 марта 2019, 19:22 +03:00 от Szilárd Páll : > >Hi, > >First off, please post full log

[gmx-users] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany

Dear list subscribers, we are very delighted to remind you about this year’s “33rdMolecular Modelling Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, Monday 8th to Wednesday 10th, 2019, at the Friedrich-Alexander-University in Erlangen, Germany. Please notice that re