Hi gromacs user
I am simulating protein ionic liquid(IL) system, in my IL forcefield the
function type of dihedral parameter is 5. When I am running
gmx mdrun it appears the following error.
Program: gmx mdrun, version 2018.1
Source file: src/gromacs/topology/topsort.cpp (line 139)
Fatal er
Dear experts,
I have an issue to re-scale the x-axis on DSSP graph eps format for my 100
ns simulation time.
The x-axis of the graph became too compact until it can't be read clearly.
How should I solve this? Is there anyway to re-scale the graph for eps
format.
Your help is much appreciated. T
Hi Mark,
Thank you for your response.
Here are the part of options that gmx energy gives me out:
9 Coulomb-(SR)10 Coul.-recip.
11 Flat-bottom-posres 12 Potential
13 Kinetic-En. 14 Total-Energy15 Conserved-En
Energy
Dear All,
I am facing an issue I do not fully understand. Namely, let's take two
crystallographic structures of the same protein and in one of them let's
delete three crystallographic water molecules that are not buried inside
the protein (let's forget about a reason for it for a moment).
Now, wh
dear all,
I am trying to improve the GAFF2 dihedral parameters for a torsion on a
small molecule. My small molecule has 5 torsions, only one is problematic,
I have been able to improve the dihedral parameters for the other 4
torsions by adjusting the force constants of the GAFF2 dihedral terms.
I
Hi,
On Mon, 9 Sep 2019 at 12:01, Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
wrote:
> Dear all,
> I am running REMD simulation with 65 replicas. When the
> simulation is running , I checked the .log file for every replica. In some
> replicas I am getting more than 10% load imbalanc
Hi,
What does the log file detection output contain? You might have linked
against a CUDA release not compatible with your drivers (e.g. too
recent).
Cheers,
--
Szilárd
On Sun, Sep 8, 2019 at 5:17 PM Mahmood Naderan wrote:
>
> Hi
> With the following config command
> cmake .. -DGMX_GPU=on -DCMA
Dear all,
I am running REMD simulation with 65 replicas. When the
simulation is running , I checked the .log file for every replica. In some
replicas I am getting more than 10% load imbalancing. How to solve that. If
I use -ntmpi and -ntomp option ..mdrun is throwing a fatal error
Fat
