On Tue, Jun 25, 2013 at 1:34 AM, S. Alireza Bagherzadeh
wrote:
> Dear All,
>
> I have a box of 3073 tip4p water molecules. I do a 250ps nvt, then 250 ps
> npt and finally a 1 ns nve (production run).
>
> I used the opls forcefield and I copied the tip4p.itp to my working
> directory (in order to b
For my system reducing shake-tol greatly improves the energy conservation
generally 1.0e-7 is the largest I would use. However if you want very good
energy conservation 1.0e-9 or lower might be needed.
This effect might only be for my system but I think it might help here too
Richard
On 25/06/20
Dear Users,
I know this error has been discussed many times but the outcome from
mdrun -pf and -px stopped at the same time which is 39470 ps. Somehow
gromacs caanot read pullx500.xvg but no clue why. I tried dos2gmx and still
the same error occur.
As I do not care about pullx500.xvg I run grompp
Dear Gromacs developers/users,
After suggestions on this mailing list to use intel over gcc compilers, we
recently obtained the newest intel compilers (2013.4.183). I was kind of
disappointed to find that there is no speed-up at all when comparing a gcc and
intel compiled g4.6.2. Is this expect
I had this some time ago and cant remember everything, other than its a format problem. My end solution that worked was to simply cut and past in columns the entire pullf into one .xvg, say in gnumeric retaining an origional header, than read it into xmgrace, and then just write it out from xmgra
Sir,
I did an remd simulation in implicit solvent for a peptide.I want to
compare the NOE distances from NMR and various conformations from REMD
output. Here how I get various conformations from remd trajectory? .Is any
script is available to find distance between two particular atoms?.How
On Tue, Jun 25, 2013 at 12:11 PM, Djurre de Jong-Bruinink
wrote:
> Dear Gromacs developers/users,
>
> After suggestions on this mailing list to use intel over gcc compilers, we
> recently obtained the newest intel compilers (2013.4.183). I was kind of
> disappointed to find that there is no spee
Sure, worth trying.
Mark
On Tue, Jun 25, 2013 at 10:07 AM, Broadbent, Richard
wrote:
> For my system reducing shake-tol greatly improves the energy conservation
> generally 1.0e-7 is the largest I would use. However if you want very good
> energy conservation 1.0e-9 or lower might be needed.
>
>
There's number of analysis tools briefly described in chapter 8 of the
manual, and lots more detail in Appendix D. Have a look at what is
there, and do your background reading of the literature to see the
kinds of things people have done before you.
Mark
On Tue, Jun 25, 2013 at 1:18 PM, Shine A
Dear all,
I would like to calculate the generalized correlation (Lange and Grubmueller,
2006). But it seems that available source code (g_correlation) is
compatible only with GROMACS-3.x.
Please can anyone provide g_correlation tool which can read tpr and xtc
files generated using GROMACS-4.5.x.
Thank you for this.
I run this simulation from scratch, will try it next time thought.
Steven
On Tue, Jun 25, 2013 at 11:26 AM, lloyd riggs wrote:
> I had this some time ago and cant remember everything, other than its a
> format problem. My end solution that worked was to simply cut and past
Dear users,
How can i fix the system structure while minimizing energy ? I made a
larger system by double a small system. But i can not continue simulation
because the system crashed after EM. Although the small system was
equilibrated well before doubling.
Thankful for any help and regards,
Th
Usually this means your "doubling" didn't allow for the required space
between atoms at the boundaries. It is usually less painful for a
solute+solvent system to go back to your solute-only coordinate file,
put a box around it with editconf, replicate that with genconf, and
only then get solvent in
On Tue, Jun 25, 2013 at 8:53 AM, Mark Abraham wrote:
> You're using a real-MPI process per core, and you have six cores per
> processor. The recommended procedure is to map cores to OpenMP
> threads, and choose the number of MPI processes per processor (and
> thus the number of OpenMP threads per
On Tue, Jun 25, 2013 at 5:46 PM, Pedro Lacerda wrote:
> On Tue, Jun 25, 2013 at 8:53 AM, Mark Abraham wrote:
>
>> You're using a real-MPI process per core, and you have six cores per
>> processor. The recommended procedure is to map cores to OpenMP
>> threads, and choose the number of MPI processe
Dear all
I did some bio simulation by dl_poly ,is it possible use gromacs for analysis
data?
Best Of Luck
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Hi Justin,
Thank you for your answer. I’m performing several tests to see what is the
best for my system. The reason I decided not to couple the intramolecular
interactions is because I think that the annihilation of the molecule will
lead to very extreme configurations and that will affect my ph
Hello everyone,
For a system of water (SOL) and ion (NA), if a speical potential needs to be
applied only to
SOL and NA, we have to make a user-define tabulation potental table_SOL_NA.xvg.
And then the
table.xvg is for the other groups of SOL SOL and NA NA.
Here is the question, for groups of S
Hi gmx-users,
I used 8-cores AMD CPU with a GTX680 GPU [ with 1536 CUDA Cores] to
run an example of Umbrella Sampling provided by Justin.
I am happy that GPU acceleration indeed helps me reduce significant time (
from 34 hours to 7 hours) of computation in this example.
However, I found th
Hi Everyone,
I'm very interested in using a set of recently derived AMBER heme
topologies within GROMACS to perform MD simulation on P450 enzymes.
Specifically I would like to use parameters found here
https://gist.github.com/anonymous/995efe4d44c6cf0584ef
After trying to use topolbuild1.3, foun
On Wed, Jun 26, 2013 at 1:16 AM, Parker de Waal
wrote:
> Hi Everyone,
>
> I'm very interested in using a set of recently derived AMBER heme
> topologies within GROMACS to perform MD simulation on P450 enzymes.
>
> Specifically I would like to use parameters found here
> https://gist.github.com/ano
Hi Mark,
That was silly mistake on my part... thank you for pointing that out.
Now I've been able to successfully convert the two .mol2 files into gromacs
.itp however I am unsure how to convert the .frcmod file as well.
Cheers,
Parker
On Tue, Jun 25, 2013 at 7:57 PM, Mark Abraham wrote:
> On
Hi, Sonia-
Gromacs 4.6.2 (some bug fixes vs 4.6.1) with the example files you
point out from Alchemistry.org should work well for expanded ensemble.
David Mobley and I have been validating expanded ensemble and replica
exchange, and the files posted there now are stable for all sizes of
systems,
On 6/25/13 4:36 PM, Sonia Aguilera wrote:
Hi Justin,
Thank you for your answer. I’m performing several tests to see what is the
best for my system. The reason I decided not to couple the intramolecular
interactions is because I think that the annihilation of the molecule will
lead to very extr
On 6/25/13 6:33 PM, Dwey wrote:
Hi gmx-users,
I used 8-cores AMD CPU with a GTX680 GPU [ with 1536 CUDA Cores] to
run an example of Umbrella Sampling provided by Justin.
I am happy that GPU acceleration indeed helps me reduce significant time (
from 34 hours to 7 hours) of computation
Please keep all Gromacs-related questions on the gmx-users mailing list. I am
not a private help service.
On 6/26/13 12:05 AM, Dwey wrote:
HI Justin,
Thanks for your suggestions about GPU/CPU load imbalance.
I actually dug into Archive. It concludes that a single and faster GPU is better
On 2013-06-25 21:52, hamid mosaddeghi wrote:
Dear all
I did some bio simulation by dl_poly ,is it possible use gromacs for analysis
data?
Best Of Luck
sure,if you can output the sim as e.g. a pdb file with multiple
frames/models. Some analysis tools need a gromacs topology file which is
e
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