Hi,
I've never seen that error. I hope you have a compelling scientific reason
for installing such a slow old version :-)
Mark
On Oct 31, 2014 1:58 AM, "Agnivo Gosai" wrote:
> Dear Users
>
> I compiled double precision Gromacs 4.5.6 in my university cluster ( named
> CyEnce ).
> It is the seria
Mdrun reports its version, yes?
Mark
On Oct 31, 2014 7:14 AM, "lloyd riggs" wrote:
>
> Im getting a "Attempting to read a checkpoint file of version 15 with code
> of version 12", does anyone know off hand which is version 12 ? Im guessing
> lik 4.5.6 , but dont know.
>
> Stephan Watkins
>
> --
Im getting a "Attempting to read a checkpoint file of version 15 with code of version 12", does anyone know off hand which is version 12 ? Im guessing lik 4.5.6 , but dont know.
Stephan Watkins
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mai
even using PLUMED plugin?
On Wed, Oct 29, 2014 at 1:59 PM, David van der Spoel
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 Spoel,
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 :-
http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Clust
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 Pharmaceuti
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:
http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.
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:
http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.
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 throug
On Thu, Oct 30, 2014 at 2:39 PM, Turgay Cakmak
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 any possible overl
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 t
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 tru
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 t
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 r
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 be
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 d
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, mimic
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 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 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?"
Pl
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 a
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
the
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 PM
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 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 correc
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 error.
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
http://pubs.
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
wrote:
> On 2014-10-30 07:27, weiduo zhu wrote:
>
>> Dear sir,
>>
>> I’m trying to simul
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 lo
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