Re: [gmx-users] lincs warning

Hi Afsane, You need to provide more details of the simulation, such as how you generated the configuration and topology, what force field you used and so on, or we can not give you any advice. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip:

Re: [gmx-users] gromacs installation (2020&2019)

Hi Netaly, Although I do not know the exact reason of the failure, after skimming through your command, I think that you probably need to assign absolute path to CMAKE_INSTALL_PREFIX and have access to the internet for downloading REGRESSIONTEST and FFTW package. If you are new to GROMACS, I

[gmx-users] How to report bugs or issues?

-Original Messages- From: "Paul bauer" Sent Time: 2020-03-25 00:40:13 (Wednesday) To: gromacs.org_gmx-users@maillist.sys.kth.se, "gmx-annou...@gromacs.org" Cc: Subject: [gmx-users] GROMACS has switched to use Gitlab Hello gmx users! I just finished the transition of our project

Re: [gmx-users] How to solve the "LINCS WARNING" problem

#mols Protein_chain_A 1 LIG 1 SOL 30059 NA 4 — Is there any problem with my topology file and Is it the right order? Thank you very much b, You > 2020. 4. 17. 오후 3:34, Yu Du 작성: > > Hi Jinyoung, > >

Re: [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals

Hi Micholas, Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology

Re: [gmx-users] Measuring bond distances, angles and dihedrals

Hi Robert, Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice.

Re: [gmx-users] How to solve the "LINCS WARNING" problem

Hi Jinyoung, You made it clear. If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand. To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process

Re: [gmx-users] Measuring bond distances, angles and dihedrals

Hi Robert, I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system,

Re: [gmx-users] How to solve the "LINCS WARNING" problem

de some details of the generation of ligand's topology” Du you mean that I modify my topology file manually?? > 2020. 4. 14. 오후 5:08, Yu Du 작성: > > Hi Jinyoung, > > I guess that the LINCS WARNING you encountered maybe came from hiden errors > in the configuration of either p

Re: [gmx-users] GROMACS PBS GPU JOB submission

Hi Tuanan, I think your problem can be separated into several parts: First, use one PBS script contains 4 GMX commands, shown as follows, may solve your problems: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod1.tpr

Re: [gmx-users] How to solve the "LINCS WARNING" problem

Hi Jinyoung, I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring.