Hi Alan , Oliver
I have obtained the gromacs format files by amb2gmx.pl script, but I am
not sure if this flies are correct ,
because all of the [pairs](1-4 interaction) are zero in gromacs top files. I
don't know whether this files are correct or not.
Would you give me some advice?
On 25/12/10 02:12, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get the
correct ensemble. Could you tell me?
As far as I know v-rescale should generate a correct
Dear All
I want to generate .top and .gro files for protein-ligand complex.
there are many problems,can every body guide me?
Actually it is my M.sc thesis and it has taken much time of me.
problems:
1-after using PRODRG server the vector boxes for are not the same
2-ligand's coordinates change
Unfortunately I am neither a free help service, nor know anything about
membrane simulations.
Please consider reading some textbook and/or tutorial material (search
the web) and please ask focussed questions on an appropriate mailing list.
Mark
Original Message
Subject:
On 25/12/2010 2:32 PM, shikha agarwal wrote:
hello
Merry Christmas.
this is my topol_pope.top file
; Include chain topologies
#include forcefield.itp
#include pope.itp
; Include water topology
#include spc.itp
; Include ion topologies
#include ions.itp
; System specifications
[ system ]
I'm not sure, since actually kinetic energy should have fluctuation, and the
v-rescaling may suppress the fluctuation..
2010/12/25 ms deviceran...@gmail.com
On 25/12/10 02:12, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's
On 25/12/2010 11:03 PM, mustafa bilsel wrote:
Hi Justin,
maybe I am making a mistake with installation. What I am doing is this:
I am creating a diretory called DSSP, then I write
rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/
/home/m/DSSP/
on the terminal, and then
On 25/12/2010 11:21 PM, mohsen ramezanpour wrote:
Dear All
I want to generate .top and .gro files for protein-ligand complex.
there are many problems,can every body guide me?
Actually it is my M.sc thesis and it has taken much time of me.
Yep, research is difficult and time-consuming and hard
On 25/12/2010 1:12 PM, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble,
and that's the reason why I used it. I wonder whether v-rescale can
also get the correct ensemble. Could you tell me?
I'm quite curious how to choose the frequency of
Dear All
How can we measure the distance between COM of two molecules?of course in
vector form!
thanks in advance
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear all,
Merry Xmas! I have a very quick question here which i'd like to pick your brain
on, would really appreciate a reply.
I am planning to replicate an experiment that I have carried out. Just
wondering what is the best way to do it? I am thinking of changing the starting
velocity of
Yeah! Energy minimization with pressure coupling.
Is this possible?
Ting
On 12/24/2010 5:04 AM, Terry wrote:
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 24/12/2010 5:17 AM, MyLinkka wrote:
Does anybody
On 2010-12-25 15.05, NG HUI WEN wrote:
Dear all,
Merry Xmas! I have a very quick question here which i'd like to pick
your brain on, would really appreciate a reply.
I am planning to replicate an experiment that I have carried out. Just
wondering what is the best way to do it? I am thinking of
Hi Mark,
Forgive me asking a question that may be obvious for experienced GMX users.
I want to quickly verify a problem against some other software, so I
temporarily turn to Gromacs.
It would be nice if you could point me out where to find the relevant tutorial
or manual chapter.
I couldn't
Mark Abraham wrote:
On 25/12/2010 2:32 PM, shikha agarwal wrote:
hello
Merry Christmas.
this is my topol_pope.top file
; Include chain topologies
#include forcefield.itp
#include pope.itp
; Include water topology
#include spc.itp
; Include ion topologies
#include ions.itp
; System
MyLinkka wrote:
Yeah! Energy minimization with pressure coupling.
Is this possible?
No. There are no velocities in EM, and hence no kinetic energy, no virial, and
thus no pressure coupling.
-Justin
Ting
On 12/24/2010 5:04 AM, Terry wrote:
On Fri, Dec 24, 2010 at 5:36 AM, Mark
On 25/12/10 02:12, Qin Qiao wrote:
Thanks a lot!
It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get
the
correct ensemble. Could you tell me?
As far as I know v-rescale should generate a correct
Thank you David for your prompt and useful reply :) I am in fact simulating a
membrane protein.
It's good to know I can use the generate-new-starting-velocity method. But,
do you mind to elaborate a bit more what you mean by if you simulate long
enough?
I would like to try your suggestion
Hi Alan , Oliver
I have obtained the gromacs format files by amb2gmx.pl script, but I am
not sure if this flies are correct ,
because all of the [pairs](1-4 interaction) are zero in gromacs top files. I
don't know whether this files are correct or not.
Would you give me some advice?
On 12/25/10 6:37 PM, NG HUI WEN wrote:
Thank you David for your prompt and useful reply :) I am in fact simulating a
membrane protein.
It's good to know I can use the generate-new-starting-velocity method. But, do you mind
to elaborate a bit more what you mean by if you simulate long enough?
Got it, thanks very much David!
:)
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
Sent: Sun 12/26/2010 5:55 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment
On 12/25/10 6:37 PM, NG HUI WEN wrote:
Dear users,
I did nvt equil and after that npt equilbriation and i am
using parinello rahman as the barostat but the prob is even after 200 ps of
equil the avg pressure is 1.5 bar .can anybody hepl me out with the
issue.Any suggestions please.
sree.
--
gmx-users mailing list
hello ,
this is my ions.itp file for gromos53a6 forcefield
[ moleculetype ]
; molnamenrexcl
CU11
[ atoms ]
; idat typeres nr residu nameat name cg nrcharge mass
1CU1+1CU1CU 11 63.54600
[ moleculetype ]
; molnamenrexcl
CU
Have a look at the rtp file of the force field u r using for correct
representation of the ion used..
With regards,
J. John Wesly,
FInal Year, B.Tech., Bioinformatics,
School of Chemical and Biotechnology,
SASTRA University, Thanjavur,
Tamil Nadu, India.
~WesFaith~
He who desire to learn,
http://biskit.pasteur.fr/install/applications/dssp
wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip
unzip dsspcmbi.zip
cd dssp
./DsspCompileGCC
cd ..
sudo mv dssp /usr/local/src/
cd /usr/local/bin
sudo ln -s ../src/dssp/dsspcmbi .
lina
On Sat, Dec 25, 2010 at 8:45 PM, Mark
25 matches
Mail list logo
