Thanks for the suggestions. I can see how a smaller dt would probably be
the most general approach to use as it should work with just about any
reasonable combination of settings.
-- Josh
On Tue, 2011-05-31 at 11:02 +1000, Mark Abraham wrote:
> On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:
> >
The following mdp file produces a successful dynamics run out to 100K
steps / 200 ps. What I discovered is this:
Using the md integrator, it is necessary to turn off pressure coupling.
However, pressure coupling works with sd (Langevin) integrator.
Mike
---
; title and include files
title
Hi,
I was wondering whether Gromacs can be used to perform simulation using
Dreiding force field developed by Goddard and co-workers ( J.Phys.Chem.
,94,8897,1990). If someone can share some experience in porting this force
field
in gromacs, that will be very helpful.
Sanku--
gmx-users mail
Thanks. I got it.
I was using gnuplot before.
-Swarnendu
On Tue, May 31, 2011 at 3:45 PM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:
> On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote:
> > Hello everybody,
> >
> > I have a question ragarding the unit of translational and
On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote:
> Hello everybody,
>
> I have a question ragarding the unit of translational and rotational
> energy. I am using the gromacs-4.0.7 version and it gives these units
> in the ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the
> co
Hello everybody,
I have a question ragarding the unit of translational and rotational energy.
I am using the gromacs-4.0.7 version and it gives these units in the
ektran.xvg and ekrot.xvg as "kJ mol\S-1\N" after I used the command" g_traj
-f traj.trr -s topol.trr -ekt ektrans.xvg -ekr ekrot.xvg.
I
Andrew DeYoung wrote:
Hi,
In molecular dynamics I have learned that there are three main phases:
energy minimization, equilibration (say, 2 ns in duration), and
production/dynamics (say, 3 ns in duration). Suppose that I want my
production run to use the same conditions as equilibration. Wha
Hi,
In molecular dynamics I have learned that there are three main phases:
energy minimization, equilibration (say, 2 ns in duration), and
production/dynamics (say, 3 ns in duration). Suppose that I want my
production run to use the same conditions as equilibration. What is the
best way to do th
Hyunjin Kim wrote:
Hi,
I included a small organic moelcule using separating .itp and .rtp files
in charmm36.
If I ran pdb2gmx to generate top file, it generated properly.
However, although I included 256 molecules, it still treated them as one
molecule as follows:
[ molecules ]
; Compound
Hyunjin Kim wrote:
Hi,
I forgot my password to access the mailing list site.
What should I do to fix this?
You can get a password reminder at:
http://lists.gromacs.org/mailman/listinfo/gmx-users
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS D
Hi,
I included a small organic moelcule using separating .itp and .rtp files
in charmm36.
If I ran pdb2gmx to generate top file, it generated properly.
However, although I included 256 molecules, it still treated them as one
molecule as follows:
[ molecules ]
; Compound#mols
Orgainic
Hi,
I forgot my password to access the mailing list site.
What should I do to fix this?
Thanks.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before postin
Thanks for you prompt reply - I'll try that and post back.
-SA
On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul wrote:
>
>
> Shay Teaching wrote:
>
>> Dear gromacs users,
>>
>> I am trying to pull a ligand out of a cavity of a membrane protein (along
>> the Z axis).
>> Problem is, that with eve
Hi Tsjerk,
Thank you for the response. I am sorry for the bad email structure
which was messed up when I copy it from microsoft word to my email
editor.
The error message from gromacs i think comes from the multiplicity
of HA-CA-CB-OH dihedral. In amber ff99sb force field, this dihedra
Shay Teaching wrote:
Dear gromacs users,
I am trying to pull a ligand out of a cavity of a membrane protein
(along the Z axis).
Problem is, that with every pull settings I have tried the ligand gets
"stuck" on the protein's center of mass. How can I make it go all the
was to the bulk water?
Dear gromacs users,
I am trying to pull a ligand out of a cavity of a membrane protein (along
the Z axis).
Problem is, that with every pull settings I have tried the ligand gets
"stuck" on the protein's center of mass. How can I make it go all the was to
the bulk water?
It always gets stuck on the
shahid nayeem wrote:
Dear Gromacs Users
I want to study thermal unfolding of protein in gromacs. One way to do
is to simulate at different temperature. What I want to do is to
gradually increase temperature after each n number of steps and collect
the n' number of frame for each temperature
Dear Gromacs Users
I want to study thermal unfolding of protein in gromacs. One way to do is
to simulate at different temperature. What I want to do is to gradually
increase temperature after each n number of steps and collect the n' number
of frame for each temperature interval. If I can do this
leila karami wrote:
Dear gromacs users
I want to know how to cite gromacs version 4.0.7? what paper do relate
to that?
Reference 5 in the manual. Note that information on how to cite Gromacs is
provided on p. iv of the manual, as well.
-Justin
--
===
Dear gromacs users
I want to know how to cite gromacs version 4.0.7? what paper do relate to
that?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before postin
Please post all Gromacs-related questions to the gmx-users list. I am not a
private help service. I am CC'ing the message to the list and would ask that
all further discussion be posted there.
The plot you showed was simply hydrogen bonds between some molecule and FAD,
which can easily be
shiva birgani wrote:
Dear all
I have simulated two different proteins (A and B). I need to compare
their flexibility. RMSF help to examine their flexibilty individually,
but I want to campare them with each other.
Do anybody know a solution to this? Would you please help me in this regard?
Ya , I have tried with this server, but I am getting those residues whose
side chains are present inside the barrel. Then in no way phosphate ion can
bind to the barrel, as per the protein design rules..
On Tue, May 31, 2011 at 1:33 AM, Francesco Oteri
wrote:
> Dear bharat,
> you can try Phosfin
Dear bharat,
you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a
website that predict phosphate binding site on protein stucture.
The paper url is:http://www.ncbi.nlm.nih.gov/pubmed/21622655
Il 31/05/2011 02:06, bharat gupta ha scritto:
thanks ...
On Mon, May 30, 2011 at 5:0
Dear all
I have simulated two different proteins (A and B). I need to compare their
flexibility. RMSF help to examine their flexibilty individually, but I want
to campare them with each other.
Do anybody know a solution to this? Would you please help me in this regard?
Regards
Shiva
--
gmx-users
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