Dear users:
does anybody know if the presence of either CPU-to-GPU or GPU-to-GPU nvlink
affects the performance or efficiency of gromacs?
Thank you,
Chris.
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On 3/28/17 2:59 PM, gozde ergin wrote:
I use Charmm36 force field. Do you mean the force field parameter between
cocobetaine and SDS? Because for pure surfactant I am able to estimate the
correct surface tension. Which means force field parameter of SDS-water and
cocobetaine-water is fine.
S
I use Charmm36 force field. Do you mean the force field parameter between
cocobetaine and SDS? Because for pure surfactant I am able to estimate the
correct surface tension. Which means force field parameter of SDS-water and
cocobetaine-water is fine.
Sent from my iPhone
> On 28 Mar 2017, at 7
Fixed charges may work as well, although some parameterization might be
necessary.
there are plenty of papers reporting such simulations, for instance:
Langmuir, 2015, 31 (48), pp 13127–13137
*DOI: *10.1021/acs.langmuir.5b03167
On Tue, Mar 28, 2017 at 2:27 PM, Michael Brunsteiner
wrote:
> > A
It worked.
Thanks Justin.
2017-03-27 18:23 GMT-03:00 Justin Lemkul :
>
>
> On 3/27/17 5:17 PM, Graziele Bortolini wrote:
>
>> The error 3 was solved, but when I change to cutoff-scheme = group, I
>> receive:
>>
>> "Fatal error:
>> The largest charge group contains 66 atoms. The maximum is 32."
>>
> Anjali Patel wrote:> What is the procedure of using gromacs specially for
> inorganic compound??> I am beginner for gromacs simulation package, I used it
> for organic
> compounds. But unable to understand how to deal with inorganic compounds
> and what about the force field and solvent we can
On 3/28/17 12:43 PM, gozde ergin wrote:
I have a mixed system of SDS and cocobetaine on water surface.
I estimated the surface tension of SDS on water surface and cocabetaine on
surface tension separately and correctly (comparing with experimental results).
However I could not estimate the cor
On 3/28/17 12:17 PM, Poncho Arvayo Zatarain wrote:
Hello gromacs user: I want to obtain the msd and lateral diffussion for
dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc
-lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2
& 3 are dppc and d
I have a mixed system of SDS and cocobetaine on water surface.
I estimated the surface tension of SDS on water surface and cocabetaine on
surface tension separately and correctly (comparing with experimental results).
However I could not estimate the correct surface tension for SDS-cocobetaine
mi
Hello gromacs user: I want to obtain the msd and lateral diffussion for
dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc
-lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 &
3 are dppc and dppe. Wht do you think about my command? It´s ok or i
- Message from Mark Abraham -
Date: Tue, 28 Mar 2017 12:04:42 +
From: Mark Abraham
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic
SASA separately in latest version of gromacs?
To: gmx-us...@gromacs.org
H
Yeah. Thank you Mr.Justin
On Tue, Mar 28, 2017 at 7:43 PM, Justin Lemkul wrote:
>
>
> On 3/28/17 10:06 AM, RAHUL SURESH wrote:
>
>> But in case of charmm36ff, the script file will not generate .gro file for
>> ligand I believe. In that case how will i generate gro file?
>>
>>
> I responded to y
On 3/28/17 10:06 AM, RAHUL SURESH wrote:
But in case of charmm36ff, the script file will not generate .gro file for
ligand I believe. In that case how will i generate gro file?
I responded to your exact same question yesterday. Please read that.
-Justin
On Tue, Mar 28, 2017 at 5:28 PM,
But in case of charmm36ff, the script file will not generate .gro file for
ligand I believe. In that case how will i generate gro file?
On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul wrote:
>
>
> On 3/27/17 11:49 PM, RAHUL SURESH wrote:
>
>> How will I add ligand .gro file in protein .gro file
I suggest trial and error in quite short runs without wasting time on waiting
for next day or so. Really large k can create segmentation faults or
"cannonball into wall" like effects in MD movie.
On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary
wrote:
Hi all,
I am trying to pul
Hi,
Avoiding these kind of artefacts is exactly why the recommended procedure
is to follow
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
Mark
On Tue, Mar 28, 2017 at 2:02 PM Justin Lemkul wrote:
>
>
> On 3/28/17 4:26 AM, Erik Marklund wrote:
> > Dear Yvon,
> >
> > Are you su
Hi,
Did
http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas
help?
Mark
On Tue, Mar 28, 2017 at 7:31 AM wrote:
>
>
>
> -- Forwarded message --
> From: sp...@iacs.res.in
> To: gmx-us...@gromacs.org
> Cc:
> Bcc:
> Date: Fri, 24 Mar 2017 16:24:21 +0530
> S
On 3/28/17 6:07 AM, Ahmet Yıldırım wrote:
Dear users,
I was trying to do the free energy calculation on GROMACS-2016.1 but I
faced a problem. To apply intermolecular restraints I add the [
intermolecular_interactions ] part at the end of complex topology file.
First I turn off intermolecular i
On 3/28/17 5:00 AM, Anjali Patel wrote:
What is the procedure of using gromacs specially for inorganic compound??
I am beginner for gromacs simulation package, I used it for organic
compounds. But unable to understand how to deal with inorganic compounds
and what about the force field and solv
On 3/27/17 11:51 PM, RAHUL SURESH wrote:
So it is mandatory to add
*; Include ligand topology
#include "drug.itp"*
In top file.?
You can't simulate a drug molecule without telling grompp what it's parameters
are so that mdrun can simulate it.
-Justin
On Tue, 28 Mar 2017 at 2:08 AM,
On 3/27/17 11:49 PM, RAHUL SURESH wrote:
How will I add ligand .gro file in protein .gro file to make a complex .?
With a text editor. Go through my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-Justin
On Tue, 28 Mar 2017 at 2:12 AM
On 3/28/17 4:26 AM, Erik Marklund wrote:
Dear Yvon,
Are you sure you ‘re not constraining, say, H-bonds in one and not the other?
This is almost certainly the case. We've done extensive validation of CHARMM
vs. GROMACS energies and the agreement is nearly perfect if calculated properly.
On 3/28/17 3:12 AM, Simon Kit Sang Chu wrote:
Dear Justin,
Thank you very much. I followed the same spirit and add forcefield.doc.
However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc
files into aminoacids.rpt .ddb . GROMACS seems to recognize only the
name "aminoacids"
On 3/27/17 11:34 PM, Dilip H N wrote:
Sorry it was a typing mistake..it is actually
1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx
del 2
Removed group 2 'SOL'
> del 1
Removed group 1 'Water'
> del 0
Removed group 0 'System'
a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0
Hi all,
I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate
Hi All,
{apologies if posted multiple times; seems like some trouble with my
account}
I want to pull linear molecule across the membrane in two ways allowing:
- translation along Z and rotation around Z
- translation along Z and rotation in all axes
My current mdp-setting pulls molecular along Z
Dear users,
I was trying to do the free energy calculation on GROMACS-2016.1 but I
faced a problem. To apply intermolecular restraints I add the [
intermolecular_interactions ] part at the end of complex topology file.
First I turn off intermolecular interactions and then turn them on one by
one.
Done! https://redmine.gromacs.org/issues/2148
On 28 Mar 2017, at 10:24, Erik Marklund
mailto:erik.markl...@kemi.uu.se>> wrote:
Hi Mark,
Thanks. I will do so once my collaborators confirm that it’s ok that I upload
the structure files.
Kind regards,
Erik
___
Thanks Peter and Mark!
I'll try running on single cores ...
however, comparing the timings I believe the bottleneck might be the time spent
in I/O(reading/writing to disk) and here running several jobs on a single node
with multiple coresmight make things even worse.
also funny: In the log files
What is the procedure of using gromacs specially for inorganic compound??
I am beginner for gromacs simulation package, I used it for organic
compounds. But unable to understand how to deal with inorganic compounds
and what about the force field and solvent we can use.
With regards
Anjali Patel
Hi All and thank you Mark for your answer,
I created a vector with make_ndx between 2 atoms but I can't find how to use
this vector with the editconf command. The "rotate" option needs for a vector
representing the rotation around axis Z ( 0 , 0 , 60) but the result seems not
to be of this ampl
Dear Yvon,
Are you sure you ‘re not constraining, say, H-bonds in one and not the other?
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi
Hi Mark,
Thanks. I will do so once my collaborators confirm that it’s ok that I upload
the structure files.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 453
Dear Justin,
Thank you very much. I followed the same spirit and add forcefield.doc.
However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc
files into aminoacids.rpt .ddb . GROMACS seems to recognize only the
name "aminoacids". Also, don't forget to change the ffPACE1.5.itp t
The correct value for kcal conversion is 4.184, however that does not
explain the difference. Maybe you can try to take one exampel, e.g. the
first one and test it bond by bond (by turning on one term at a time in
the topology). I assume this is for 0 steps of MD or EM?
Den 2017-03-28 kl. 07:
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