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" wrote:
> /I am trying to use pdb2gmx to get a topology for a very simple peptide
> that
> has just three compo
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
horr
Hi all,
I'm working on a single server with 2 Intel Xeon E5-2660
processors. Each processor has 8C/16T, so total 16C/32T.
I want to utilize both the processors for my simulation, thread MPI/
multithreading doesn't work as I'm doing calculations using plumed
patch which supports the use of only 1
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
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 command to got the free energy landscapes. do
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 I
Define large fluctuations. They might be physical large fluctuations!
On Thu, Nov 28, 2013 at 1:19 AM, bipin singh 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 lamda values viz.
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 like
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 comman
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 wrote:
> Define large fluctuations. They might be p
dear timo
Please send me further details. I'm not a professional.
Thanks and regards
On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote:
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 liga
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight wrote:
> 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 si
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 molecules，it give me a Fatal error:
Fatal error:
Death
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 T
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 b
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 mol
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 s
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
wrote:
> Hi all,
>
>
Oh, I am sorry, I made a big mistake! :)
Best Regards
On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul 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 mod
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 so
It's very possible that this is entirely physical. dh/dl fluctuates a
lot. You may want to look at graphs of after a few 10's of ps
to see if it looks reasonable.
On Thu, Nov 28, 2013 at 10:04 AM, bipin singh wrote:
> I am mentioning below the average and standard deviation of dh/dl values at
>
In addition to where Szilard said to look, you can also try looking for
force fields on the user contributions part of the GROMACS website:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid
parameters, this
On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote:
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?
That would be one possible solution, but it is not yet clear what the OP
i would use
genbox -cp box.pdb -cs tip4p -p topol.top -o waterTip4p.pdb
best
timo
On 11/28/2013 03:23 PM, Mahboobeh Eslami wrote:
dear timo
Please send me further details. I'm not a professional.
Thanks and regards
--
Gromacs Users mailing list
* Please search the archive at
http://www.groma
Thank you for your reply.
In this case it is easier to use -p option instead of manual modification
but both of them are possible. Of course In some cases we need to modify
.top files manually (protein-drug complex system).
Thanks again for information
On Thu, Nov 28, 2013 at 6:53 PM, Justin L
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
Hi,
both links helped:
http://www.gromacs.org/Downloads/User_contributions/Force_fields (for
ff99sb and parmbsc0 but need to check for double stranded dna)
and improved ions here:
http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d (they used
Cheatham ions with Gromacs, may need to modif
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, No
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 m
Hi everybody
i install gromacs 4.6.3 double precision and parallel
what is the best correct command for mdrun_mpi_d on single machine with
multiple processors (core=8)
thanks for your help
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Li
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 ;
n
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, Pu
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
wrote:
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 t
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