Original-Nachricht
> Datum: Wed, 18 Apr 2012 03:13:09 +1000
> Von: Mark Abraham
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Re: Questions
> On 18/04/2012 12:10 AM, lloyd riggs wrote:
> > Included below (although Im terrified youll invalidate massive para
Dear Gromacs users,
I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using
Gromacs. I have already carried out classical MD simulation for the
Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and
now have to analyse the structural changes in the Protein-Mg
On 18/04/2012 9:21 AM, Shyno Mathew wrote:
Hello Justin,
Thanks for your reply.
Now I have another question about appending the data to previous files.
I am running the simulation on a cluster and this is how the main line
on my job script looks like:
mpiexec -n 10 mdrun_dp_mpich2 -s equil_02.
On 18/04/2012 6:58 AM, sai nitin wrote:
Hi Justin,
I generated topologies of my protein using PDB2GMX (charmm27 FF) and
ligand topology using swissparam tool using Charmm force field i
included ligand.itp file in topol.top of protein. And i used docked
complex structure (protein + ligand) fr
Shyno Mathew wrote:
Hello Justin,
Thanks for your reply.
Now I have another question about appending the data to previous files.
I am running the simulation on a cluster and this is how the main line
on my job script looks like:
mpiexec -n 10 mdrun_dp_mpich2 -s equil_02.tpr -cpi equil_01.cpt
Hello Justin,
Thanks for your reply.
Now I have another question about appending the data to previous files.
I am running the simulation on a cluster and this is how the main line on
my job script looks like:
mpiexec -n 10 mdrun_dp_mpich2 -s equil_02.tpr -cpi equil_01.cpt -append yes
Initially i
Hi Justin,
I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand
topology using swissparam tool using Charmm force field i included
ligand.itp file in topol.top of protein. And i used docked complex
structure (protein + ligand) from docking analysis and generated boxed.pdb
n
Manual Appendix A.2; note that the last one among the reasons listed
for needing double will soon not be the case anymore (see verlet
scheme in 4.6 http://www.gromacs.org/Documentation/Cut-off_schemes).
--
Szilárd
2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro :
> Thank you, Szilárd.
Thank you, Mark
I will try the test that you suggest.
A related question about g_traj. If -ekr and -ekt report the KE of the
translational and rotational motion of a group, respectively, which implies
a rigid body decomposition, then I assume that the total KE calculated from
the sum of these two
Thank you, Szilárd.
Do you know where (say, in a piece of code or some documentation) I can be
sure about that?
Cheers,
Pedro.
Em 17 de abril de 2012 15:43, Szilárd Páll escreveu:
> 2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro <
> palap...@gmail.com>:
> > Hi,
> >
> > I've come acro
2012/4/17 Pedro Alexandre de Araújo Gomes Lapido Loureiro :
> Hi,
>
> I've come across a discussion about the "single X double precision" issue in
> a NAMD users list e-mail
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9166.html).
> I would like to know what do you think about these
Sangita Kachhap wrote:
Hello all
I am new for gromacs. I have to do MD simulation of membrane protein docked with
organic molecule.
I have gerated top and itp for ligand using PRODRG server also generated top
file for complex.
Hopefully you're not relying on an unrefined PRODRG topology. Se
Hello all
I am new for gromacs. I have to do MD simulation of membrane protein docked with
organic molecule.
I have gerated top and itp for ligand using PRODRG server also generated top
file for complex.
But when I am generating .tpr file for a POPC system using grompp getting an
error:
creatin
Hi,
I've come across a discussion about the "single X double precision"
issue in a NAMD users list e-mail (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9166.html).
I would like to know what do you think about these 3 specific points:
1) "there are some places where single precision (
On 18/04/2012 12:10 AM, lloyd riggs wrote:
Included below (although Im terrified youll invalidate massive parallel work
with a single comment) is the .mdp file I used for 10 of the runs, basically it
was the only way I could get it to run. The time step is small because of the
small molecule i
I solved the problem on a Linux machine, with about all the text editors, I was
stuck for days on a PC, which even the script editors couldn't spot a
difference in files. all i used was ms txteditor to cut and paste.
> I dont know. All I know is if I have it print one of the other deminsions,
Shyno Mathew wrote:
Dear all,
This is the first time I am trying to extend a run in gromacs.
I read in the gromacs website following are the steps to used for this
purpose:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
So this means I don't
Dear all,
This is the first time I am trying to extend a run in gromacs.
I read in the gromacs website following are the steps to used for this
purpose:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
So this means I don't need to modify the .mdp fi
> I dont know. All I know is if I have it print one of the other deminsions, I
> get the other curves mentioned.
>
"When accusing the code of doing something wrong, "I don't know" isn't a very
good justification ;) The contents of pullx.xvg are the COM coordinates of the
reference group on t
On 17/04/2012 7:32 AM, Roy wrote:
Mark,
According to the manual, the temperature of a group should always be
calculated from the total KE of the group (see eq 3.13 in the manual), which
presumably includes contributions from the translational motion of the
center of mass of the group, plus the
lloyd riggs wrote:
Original-Nachricht
Datum: Tue, 17 Apr 2012 07:49:06 -0400
Von: "Justin A. Lemkul"
An: lloyd riggs , Discussion list for GROMACS users
Betreff: Re: Questions
lloyd riggs wrote:
Dear Justin,
So I get no answere on the mail list so decided to ask you
Original-Nachricht
> Datum: Tue, 17 Apr 2012 07:49:06 -0400
> Von: "Justin A. Lemkul"
> An: lloyd riggs , Discussion list for GROMACS users
>
> Betreff: Re: Questions
>
>
> lloyd riggs wrote:
> > Dear Justin,
> >
> > So I get no answere on the mail list so decided to ask y
On 17/04/2012 11:12 PM, anupam sinha wrote:
Dear All,
I have tried installing gromacs (after installing fftw3
library)on a GPU system using the following :
./configure --with-fft=fftw3 --enable-float
After I type "make" I get the following error after sometime.
.
.
.
/usr/bin/
Dear All,
I have tried installing gromacs (after installing fftw3
library)on a GPU system using the following :
./configure --with-fft=fftw3 --enable-float
After I type "make" I get the following error after sometime.
.
.
.
/usr/bin/ld: /home/anupam/fftw-3.3.1/.libs/libfftw3f.a(api
lloyd riggs wrote:
Dear Justin,
So I get no answere on the mail list so decided to ask you (and most likely
Dr. Abrahams if you dont answere) some questions as follows.
Please keep all discussion on the mailing list.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Your
Kamalesh Roy wrote:
Can you send me the parameters I need to usefor FE
Most of the force fields in Gromacs have support for Fe built in, at least in
the context of heme. What is it that you're trying to do? If you need new
parameters for whatever reason, it will be very tricky to
If I just make a sub directory and move every fill (.tpr, pullf.xvg, etc... it
works, so must not be gromacs realted I appologise)
Stephan Watkins
Original-Nachricht
> Datum: Mon, 16 Apr 2012 15:35:17 +0200
> Von: "lloyd riggs"
> An: Discussion list for GROMACS users
> Betre
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