Hi all.
I am new to gromacs and my major is not related to molecular simulation so
I do not know the meaning of almost everything in the output information :(
For example, in the output file like below:
=
step 375: timed with pme grid 80
I would recommend 200,000 time steps to try to get accurate pressure readings.
Pressure, I believe, is computed from the virial and can fluctuate a lot.
Also, adjust nstcalcenergy and nstenergy to a small number, I use 10 to get
more accurate pressure readings. You should have noticed the error
Hi,
It's not about adding points. The statistics are over all time steps
already. However, it should be noted that at t=0 the pressure was not
controlled yet. So these statistics include the convergence and are
therefore unlikely to reproduce the reference pressure. In addition, there
is the
On 2014-10-30 07:27, weiduo zhu wrote:
Dear sir,
I’m trying to simulate a ethanol gas system, only one ethanol
molecule in 10*10*10nm box. but when I analysis the energy, it shows
that potential is positive, and the Coul.recip term is very positive
throughout the entire run. I think the
For a single configuration of ethanol, you can do the calculations on a
piece of paper and see if you're doing better than Gromacs.
Cheers,
Tsjerk
On Thu, Oct 30, 2014 at 8:27 AM, David van der Spoel sp...@xray.bmc.uu.se
wrote:
On 2014-10-30 07:27, weiduo zhu wrote:
Dear sir,
I’m
Dear all Gromacs users,
I am running MD simulation using Gromacs in Cluster. In my 3.5ns, it
goes smooth and after that when i view my md.log file, it shows that File
input/output error:Cannot rename checkpoint file; maybe you are out of
quota?
Please let me know how to rectify the
Hi,
to the best of my knowledge,
Molecular Dynamics is not the best way to study system stabilized by
Pi-Pi or Pi-Cataion interaction.
However,in MD people usually overpolarized C-C and C-H bonds to
increase the quadrupole interactions, and thus, mimic the Pi-Pi
interaction
See
Dear Gromacs users,
I am trying to run MD for my DNA structure, however after typing
grompp -f nvt.mdp -c em.gor -p top -o *.tpr
I am getting an error message:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
NOTE 1 [file nvt.mdp]:
The Berendsen thermostat does not generate the
Thank you both for your prompt replies.
Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
is it just by a trial-error approach?
Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it
crashes. I was thinking to run the first 2ns with 1fs and then try
Dear Ivan,
Thank you. I also think what you are saying that is right.
I will also goes through the article. Thank you for article
I actually run the system with simple Gromos96 5316 FF and amber 03 ff. I
dont think it will
help me
With regards,
Rama David
On Thu, Oct 30, 2014 at 2:27
Dear gromacs users,
I am having some problems with hbond analysis using gromacs. I am
interested in hbonds between certain amino acids for example: LYS256 and
nucleic acid that has number 2 in my files. I generated the index file
which contains r256 and r2 by running make_ndx -f gro -o out.ndx
On 10/30/14 1:19 AM, Sathish Kumar wrote:
Dear gromacs-users,
I have run the umbrella sampling with the help of
tutorial of justin. In my system rna is binding with gold nanoparticle. To
find out the binding energy, i run the umbrella sampling using the space
0.1 nm
On 10/30/14 4:55 AM, Kannan S wrote:
Dear all Gromacs users,
I am running MD simulation using Gromacs in Cluster. In my 3.5ns, it
goes smooth and after that when i view my md.log file, it shows that File
input/output error:Cannot rename checkpoint file; maybe you are out of
quota?
On 10/30/14 2:02 AM, Vinson Leung wrote:
Hi all.
I am new to gromacs and my major is not related to molecular simulation so
I do not know the meaning of almost everything in the output information :(
For example, in the output file like below:
On 10/30/14 5:22 AM, Urszula Uciechowska wrote:
Dear Gromacs users,
I am trying to run MD for my DNA structure, however after typing
grompp -f nvt.mdp -c em.gor -p top -o *.tpr
I am getting an error message:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
NOTE 1 [file nvt.mdp]:
On 10/30/14 4:57 AM, Ivan Gladich wrote:
Hi,
to the best of my knowledge,
Molecular Dynamics is not the best way to study system stabilized by Pi-Pi or
Pi-Cataion interaction.
However,in MD people usually overpolarized C-C and C-H bonds to
increase the quadrupole interactions, and thus,
On 10/30/14 7:54 AM, rama david wrote:
Dear Ivan,
Thank you. I also think what you are saying that is right.
I will also goes through the article. Thank you for article
I actually run the system with simple Gromos96 5316 FF and amber 03 ff. I
dont think it will
help me
I honestly
On 10/30/14 7:30 AM, Ioanna Styliari wrote:
Thank you both for your prompt replies.
Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
is it just by a trial-error approach?
If what Vitaly says is true, this would be a very sneaky bug that has not been
noticed
On 10/30/14 7:58 AM, Urszula Uciechowska wrote:
Dear gromacs users,
I am having some problems with hbond analysis using gromacs. I am
interested in hbonds between certain amino acids for example: LYS256 and
nucleic acid that has number 2 in my files. I generated the index file
which contains
Dear justin,
Thank you for suggestion.
I did the docking of peptide ligand and receptor and I found the
pi-pi and pi- cation interaction and hydrogen bond.
Now if I do the MD it is hard to claim the pi-pi and pi-cation
interaction through md.
If I do the md will it help me ? will
Dear Gromacs Users,
Thank you for your insightful comments. I am, however, still a bit confused
about the non-bonded terms in potential energy, so I would be happy if you
assisted me for a bit further.
Is there any possible overlap between SR and 1-4 interactions? In other
words, is it always
On 2014-10-30 13:10, Justin Lemkul wrote:
On 10/30/14 4:57 AM, Ivan Gladich wrote:
Hi,
to the best of my knowledge,
Molecular Dynamics is not the best way to study system stabilized by
Pi-Pi or
Pi-Cataion interaction.
However,in MD people usually overpolarized C-C and C-H bonds to
increase
On Thu, Oct 30, 2014 at 2:39 PM, Turgay Cakmak turgaycakma...@gmail.com
wrote:
Dear Gromacs Users,
Thank you for your insightful comments. I am, however, still a bit confused
about the non-bonded terms in potential energy, so I would be happy if you
assisted me for a bit further.
Is there
On 10/30/14 8:39 AM, rama david wrote:
Dear justin,
Thank you for suggestion.
I did the docking of peptide ligand and receptor and I found the
pi-pi and pi- cation interaction and hydrogen bond.
Now if I do the MD it is hard to claim the pi-pi and pi-cation
interaction
I am simulating an ionic liquid, and I want to generate a spatial density
map on the anion around the cation. I want an image that looks like this:
I am simulating an ionic liquid, and I want to generate a spatial density
map on the anion around the cation. I want an image that looks like this:
If you have access to 4.0.7 then you can do it, that will generate the SDF
based on multiple molecules. Unfortunately, that functionality has been
removed from the script in versions after that.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of
Dear Users
I compiled double precision Gromacs 4.5.6 in my university cluster ( named
CyEnce ).
It is the serial version as I did not compile mdrun separately as parallel
mdrun.
I followed the procedure in the below mentioned link :-
even using PLUMED plugin?
On Wed, Oct 29, 2014 at 1:59 PM, David van der Spoel sp...@xray.bmc.uu.se
wrote:
On 2014-10-29 01:05, Nizar Masbukhin wrote:
Dear gromacs users,
Is it possible to calculate free energy in implicit solvent in gromacs?
It is not possible at all.
--
David van der
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