PDB format has fixed column widths. You cannot edit it correctly unless you
preserve the layout - e.g. replace deleted characters with spaces.
Mark
On Nov 28, 2013 4:26 AM, kolnkempff kolnkem...@gmail.com wrote:
/I am trying to use pdb2gmx to get a topology for a very simple peptide
that
has
Huge forces lead to crazy displacements whose next forces are looked up
outside the boundaries of your table, which leads to a segmentation fault.
GROMACS doesn't waste its time checking for this, since that would hurt
everyone's performance and gain only a descriptive error that something is
Thank you, Mark. It makes sense.
I am using FF developed by other group, that was run in Discover before. I am
not sure I like how the plots of potentials look.
V
Huge forces lead to crazy displacements whose next forces are looked up
outside the boundaries of your table, which leads to a
Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by
gromacs4.6.3.
I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.
when I issue the grompp command to generate the necessary .tpr file
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:
Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by
gromacs4.6.3.
I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.
when
Define large fluctuations. They might be physical large fluctuations!
On Thu, Nov 28, 2013 at 1:19 AM, bipin singh bipinel...@gmail.com wrote:
Hello All,
I am trying to calculate relative solvation free energy for p-Cresol and
p-Chlorophenol using Gromacs 4.6.3.
I am using equispaced
Dear Gromacs users!
I'd like to perform replica exchange simulation
For this I've made bash script which create n folders like
replica-298
replica-312
replica-323
replica-334
...
replica-N
with all files needed for simulation considted of specified mdp file with
different ref_t value
No I'd
On 11/28/13 7:20 AM, aixintiankong wrote:
Dear, i want to make a free energy landscape with respect to Rg and RMSD.
First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate.
And the i merge the rmsd value and Rg value into one file with two column,
then i use the g_sham
Thanks for the reply.
By large fluctuations, I mean the standard deviation of dh/dl values during
the simulation at lambda 0.0 to 0.5 in comparison to lambda close to 1,
when using sc-alpha=0.5
On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts mrshi...@gmail.com wrote:
Define large
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs users!
I'd like to perform replica exchange simulation
For this I've made bash script which create n folders like
replica-298
replica-312
replica-323
replica-334
...
replica-N
with all files
Maybe you should modify your .tpr file manually according to what you added
in the previous sections!
On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com wrote:
dear timo
Please send me further details. I'm not a professional.
Thanks and regards
On Thursday,
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:
Maybe you should modify your .tpr file manually according to what you added
in the previous sections!
Manually modify a .tpr? How would one do that?
The OP needs to provide the exact commands issued. The fatal error shown
results from poor
On 11/28/13 9:31 AM, dxl...@hotmail.com wrote:
Dear All,
I'd like to do some implicit solvent MD with Gromacs. However, I meet a
trouble. For instance, I have included gbsa.itp. when I used a SPC water
molecule for Implicit Sovent MD，it goes very well. Then when I use two SPC
water
I am mentioning below the average and standard deviation of dh/dl values at
lambda=0.0 and lambda=1.0, for sc-alpha=0.5
Avg Std.
lambda0.0-2.055812e+01 2.730571e+01
lambda1.07.086960e+017.670135e+00
On Thu, Nov 28, 2013 at 7:34 PM, bipin
Yes, you can besides the minor command-line interface differences,
using MPI and thread-MPI works essentially the same way.
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#MPI.2c.c2.a0Thread-MPI
--
Szilárd
On Thu, Nov 28, 2013 at 11:07 AM, Richa Singh
Oh, I am sorry, I made a big mistake! :)
Best Regards
On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:
Maybe you should modify your .tpr file manually according to what you
added
in the previous sections!
Manually
Dear Justin
I meant modifying .top file after adding some ions and water molecules
which could be equivalent to -p option as you mentioned.
What do you think about this?
Please let me know
On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour
ramezanpour.moh...@gmail.com wrote:
Oh, I am
It's very possible that this is entirely physical. dh/dl fluctuates a
lot. You may want to look at graphs of dh/dl after a few 10's of ps
to see if it looks reasonable.
On Thu, Nov 28, 2013 at 10:04 AM, bipin singh bipinel...@gmail.com wrote:
I am mentioning below the average and standard
PS: googling AMBER FF10 + GROMACS does give (at least) one relevant
result: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d
They may have something useful and may be willing to share (and it
would certainly be useful to have it in the contrib FF section as
well).
Cheers,
--
Szilárd
Thanks for you reply Prof. Shirts.
I have plotted the dh/dl values (link mentioned below), but I am not sure
whether the fluctuation is in acceptable range at lambda=0.0. Please have a
look at the plot and let me know your thoughts.
http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png
On Thu,
Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the
.itp, should i use topolgen , and then
calculate the charges with gaussian ussing ChelpG charges, and replace it, i
was wondering if this procedure is correct, algo i´m pretending , to study
this molecule with a CNT, and a
Dear all，
I have changed the is.mdp file as following, However, the same error
still can't be removed.
What can I do for the simulation?
title = spc water
cpp = /usr/bin/cpp
;define = -DFLEXIBLE
constraints = all-bonds
integrator = md
tinit = 0
dt = 0.002 ; ps !
nsteps = 2000 ;
Dear Eslami,
Gromacs 4.6.3 can automatically take up all the cores. If you want to run
gromacs across the nodes. Then you need to compile using MPI.
Detailed instruction is available here
http://www.gromacs.org/Documentation/Installation_Instructions.
Chandan
--
Chandan kumar Choudhury
NCL,
hi
i installed openmpi and i set -DGMX_MPI=ON in cmake command.
are these casesenough?
thanks
On Friday, November 29, 2013 7:59 AM, Chandan Choudhury iitd...@gmail.com
wrote:
Dear Eslami,
Gromacs 4.6.3 can automatically take up all the cores. If you want to run
gromacs across the
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