On Mon, 28 Dec 2009, David van der Spoel wrote:
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
> bharat v. adkar wrote:
> > On Sun, 27 Dec 2009, Mark Abraham wrote:
> >
> > > bharat v. adkar wrote:
> > > >On
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
> bharat v. adkar wrote:
> > On Sun, 27 Dec 2009, Mark Abraham wrote:
> >
> > > bharat v. adkar wrote:
> > > > > >Dear all,
> >
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
> bharat v. adkar wrote:
> >
> > Dear all,
> > I am trying to perform replica exchange MD (REMD) on a 'protein in
> > water' system. I am
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos ->
REMD). I have to perform the REMD simulation with 35 different
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos ->
REMD). I have to perform the REMD simulation with 35 different
temperatures. As per advise on wiki, I equilibrated the system at
respective tempe
dear Berk,
please let us know whether following patch is correct for 3.3.1
diff orig-ns.c ns.c
2c2
< * $Id: ns.c,v 1.84.2.3 2006/03/01 07:57:46 spoel Exp $
---
* $Id: ns.c,v 1.84.2.3.1 2009/02/03 20:27:00 hess Exp $
617c617
< bool bDoVdW_i,bDoCoul_i;
---
bool bDoVdW_i,bDoCo
dear sudheer,
On Fri, 21 Mar 2008, Justin A. Lemkul wrote:
Quoting sudheer babu <[EMAIL PROTECTED]>:
Thanks for your reply,
I am mentioning commands, from crashing the simulation
1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o
out.tpr
You didn't tell tpbconv how
On Fri, 4 Jan 2008, Maik Goette wrote:
Hi
I just found a strange behaviour of GROMACS, when processing topologies with
B-values. Maybe I just think of it as unintuitive/bug, but here we go:
e.g. OPLS
Consider an angle given (all atoms have B-values, which angle-parameter can
be found by G
On Thu, 3 Jan 2008, David Mobley wrote:
OK, I seem to have traced at least the latter problems back to
something new in gromacs 3.3.2 relative to 3.3.1, in that my system
works fine in 3.3.1 but not in 3.3.2. Is there something new with
handling of constraints or settles for water in 3.3.2 rela
Hi,
I can see the curves getting overlapped after the code-modification
suggested by Berk for ethane to methane coulomb transformations in forward
and reverse directions.
Thanks Berk and David.
bharat
On Wed, 14 Nov 2007, bharat v. adkar wrote:
hi,
even i am also checking the ethane
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.
David
> Berk.
>
>
> > From: "David Mobley" <[EMAIL PROTECTED]>
> > Reply-To: Discussion list for GROMACS users
buggy.
Developers, please have a look at and confirm.
bharat
David
Hope that helps. Keep me posted on what you find.
On Nov 7, 2007 10:42 PM, bharat v. adkar <[EMAIL PROTECTED]> wrote:
Hi David,
This is regarding our discussion on gromacs mailing list on "soft-core
and cou
hi,
i am pasting the xmgrace file for the both forward and reverse
transformation of charge modification for Ala->Gly mutation.
The simulations are performed in water. when you open the file with
xmgrace, you can clearly see the behaviour what i was describing in
previous mails.
bharat
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse
transformation onto that of forward with both axes reversed. so i
should expect overlap. this is consistent with whatever you are saying. i
am sorry for negligence and confusion.
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
it is fairly straight FORWARD.. forward is from state A to state B, and
reverse is from state B to state A. Say for example, forward
transformation is going from ethane to methane. in this step, i define
three of the terminal hydrogen on say C2, with
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
Everything goes fine till this point. Now, i do reverse transformations to
check for hysteresis. For vdw transformations, i get almost perfect
overlap of dG/dlambda vs lambda for forward and reverse transformations,
but for coloumb transformations, i
Dear all,
i am trying some very basic transformations by thermodynamic integration
to calculate free energy difference. By following mailing-list archive, i
learned that it is efficient to do coulomb transformations and LJ
transformations separately. i use David Mobley's tutorial values for
Hi,
I am not sure, but think the problem might be the length of the string
PATH variable handles. check the length by "echo $PATH |wc". it will most
probably exceed the recommended length. and that is why when u give full
path on command line it works because it does not refer to the PATH.
genbox works fine for me. i use 3.3.1 version. it works fine with and
without script.
but i don't understand how will u get rid of backup files in the permanent
directory from whatever u have mentioned, because gromacs creates the
output topology in the same location where it reads the input
Dear Sampo,
rising or lowering of potential energies during md after em seems to be
fine. energy minimization will optimize for bond-lengths, bond-angles,
torsion angles to their mean values and try to get rid of any short
contacts. so basically, em will take ur starting structure to some m
Dear gromacs users,
I am trying to use FEP method for the calculation of relative binding free
energy of peptide-protein complex. I am using gmx-3.3.1.
As per previous discussions on the mailing list, i learnt that i need to
do two different sets of simulations for my case. first set will be
Thanx David...
It's working with trj and ene files though tpb is not working and i
faced no problem with tpr generated on the same system also...
as you said, even these files cannot be read on other platforms :(
bharat
On Sun, 23 Jul 2006, David van der Spoel wrote:
bharat v.
Thanx David...
It's working with trj and ene files though tpb is not working and i faced no
problem with tpr generated on the same system also...
as you said, even these files cannot be read on other platforms :(
bharat
On Sun, 23 Jul 2006, David van der Spoel wrote:
bharat v.
3.3.1
Source code file: ../../../../gromacs-3.3.1/src/gmxlib/enxio.c, line: 239
Fatal error:
Energy file ener.edr not recognized, maybe different CPU?
---
help please...
bharat
On Fri, 21 Jul 2006, bharat v. adkar wrote:
Dear GMX users,
Rec
Dear GMX users,
Recently i installed gromacs-3.3.1 on IBM powerpc64 with mpi support.
some of the details of the machines are as follows:
---
hostname = cnode39
uname -m = ppc64
uname -r = 2.6.5-7.139-pseries64
uname -s = Linux
/bin/arch= ppc64
---
Dear GMX users...
i have a protein-peptide complex wherein peptide does not have one of the
terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to
peptide and B to protein chain. when i do pdb2gmx, it adds the missing O,
so now the group is -COO. Now with this gro file, i tri
Dear GMX users,
i am trying 'relative hydration free energy of p-cresol wrt toluene' tutorial
from http://md.chem.rug.nl/education/Free-Energy_Course/3.mutation-fe.html. i am using all the mdp files given on
the site, the confout.gro from toluene/eq directory of the previous tutorial as startin
Dear Gromacs users,
I want to know that during interaction energy calculation after md run,
what dielectric constant does groamcs use? Does it use the dielectric
constant specified in the mdp file or it uses distance dependant
dielectric constant. I have given dielectric constant 1 during md ru
Dear Santosh,
check what forcefield u have used...
whatever forcefield u use, add ions as per its recommended format
specified in ions.itp. Read ions.itp carefully... if it is GROMOS96,
u have to change Na to NA+ and likewise...
all the best...
bharat
On Wed, 5 Apr 2006, santosh naik wrote:
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