Hello all,
I have been running the umbrella sampling tutorial available on the bevan
lab website.
After the following steps:
grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
-o pull.tpr
mdrun -s pull.tpr
trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
When I run the dista
On 6/23/14, 5:53 PM, ram bio wrote:
Dear Gromacs Users,
I have been trying to simulate protein-ligand complex using gromacs
versions that use verlet cutoff scheme on gpus.
These are some of the issues that i could resolve, and any kind of
suggestion or help is appreciated.
1. With gromacs 4.
Dear Gromacs Users,
I have been trying to simulate protein-ligand complex using gromacs
versions that use verlet cutoff scheme on gpus.
These are some of the issues that i could resolve, and any kind of
suggestion or help is appreciated.
1. With gromacs 4.6.5 i could simulate crystal structure f
Thank you, Dr. Shirts. My pressure coupling type is also semi-isotropic.
So is that simulation worth at all ( since equilibration not on intended
pressure even remotely) or we need to discard the simulation totally ?
Also, this high pressure (and crystal slab movement ) occurs only with
refcoord
A nonisotropic system will not necessarily end up with exactly the applied
pressure -- things like surface tension and stresses/strains end up getting
mixed in and throwing things off.
On Mon, Jun 23, 2014 at 3:32 PM, Chetan Mahajan
wrote:
> Thanks.
>
> Average was taken over 1000 ps. Error est
Thanks.
Average was taken over 1000 ps. Error estimate is 2.9 which is smaller than
average pressure of 19.87 bar. Here is the complete statistics:
Energy Average Err.Est. RMSD Tot-Drift
---
On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote:
Dear All,
First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.
I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tung
Hi,
I am trying to use the GLYCAM force-field alםng with the standard AMBER
force-field for peptides.
In doing so, there is one major concern - both force-fields use different
1-4 scaling factors.
While AMBER uses fudgeLJ = 0.8 and fudgeQQ = 0.5.
the GLYCAM force-field uses - fudgeLJ = 1.0
Dear All,
First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.
I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tungsten metal ion and some other cofactors. I
understand
On 6/23/14, 6:54 AM, Urszula Uciechowska wrote:
Dear GROMACS users,
I am working with gromacs and i have got a warning as
shown below.Can you please suggest me what to do, to run my file
completely.Please reply as soon as possible.Awaiting your suggestions.
Step 8399 Warning: Pressure scaling
On 6/23/14, 1:12 AM, Tom wrote:
Dear Gromacs Developers and Experts:
I noticed that the performance of gromacs on Cray linux clusters is only
36.7% of the normal.
Normal what? Another run on the same system? You can't directly compare
different clusters with different hardware.
The f
Dear GROMACS users,
I am working with gromacs and i have got a warning as
shown below.Can you please suggest me what to do, to run my file
completely.Please reply as soon as possible.Awaiting your suggestions.
Step 8399 Warning: Pressure scaling more than 1%.
DD step 8399 vol min/aver 0.653 load i
Dear all,
Force fields AMBER99SB-ILDNP and AMBER99SB*-ILDNP with new proline (Pro)
and 4-hydroxyproline (Hyp) dihedarl parameters are available for
downloading from
http://www.ucl.ac.uk/nmr/research
or
http://www.gromacs.org/Downloads/User_contributions/Force_fields.
Correlation times and NMR
thermodynamic ensemble has nothing to do with an average pressure value.
Dr. Vitaly V. Chaban
On Mon, Jun 23, 2014 at 7:50 AM, Chetan Mahajan wrote:
> Dear All,
>
> I am using Berendsen barostat and thermostat for NPT equilibration MD run
> at 1 atm and 300 K. While it runs fine, average pressu
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