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.
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 -
d to provide 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 configurat
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, but
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 you
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. I
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 in
ound#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,
>
-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 datab
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 r
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: 2
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