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 Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar
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
temperatures
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 following instructions given on wiki (How-Tos
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,
I am trying to perform replica exchange MD (REMD
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
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
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
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
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
, 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 coulomb transformation. Sorry for delay
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.
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
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
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
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. adkar
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
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,
Recently
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
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
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