Hi David,
I was trying to understand your comments little bit carefully. If it is a NVT
ensemble simulation, then enthalpy becomes equal to potential energy ( as the
work due to volume-change is zero ).
But, I was wondering about your other comment: i.e. if it is constraint method,
the pot
On 15/10/2010 1:12 AM, Sascha Rehm wrote:
Dear all,
to deal with my long-range interactions I used the reaction-field-zero
method. Therefore I searched for a publication of this method but did
not find a reference in the manual or on the gromacs website. Can
anybody tell me the publication o
On 14/10/2010 7:19 PM, Sathish wrote:
Dear all,
I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started
to run demo but still its running ( more then 5 hrs). How long will
take time to complete.
Any other possible way is there to increase speed ?
Anybody can help me?
It's proba
On 15/10/2010 2:54 AM, ABEL Stephane 175950 wrote:
Dear all,
I come back to you for several questions about the futures replica-exchange
calculations that i would like to perform. The system of interest will contain
12 peptides (with 7 residues each) and 4 water molecules, it come from a
Dear Florian, thanks again.
I have worked with confined systems, where motion
in a given direction/plane is preferred. The accuracy of the MSD
approach for calculating the diffusion coefficient has been
questioned for this my system. So I need to calculate
D via VACF. Considering my limited abiliti
Jyoti Mahalik wrote:
Message: 2
Date: Thu, 14 Oct 2010 21:56:22 +0200
From: David van der Spoel
Subject: Re: [gmx-users] Extracting potential energy of protein units
To: Discussion list for GROMACS users
Message-ID: <4cb76066.8050...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-
Message: 2
Date: Thu, 14 Oct 2010 21:56:22 +0200
From: David van der Spoel
Subject: Re: [gmx-users] Extracting potential energy of protein units
To: Discussion list for GROMACS users
Message-ID: <4cb76066.8050...@xray.bmc.uu.se>
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On 201
Dear all,
Thank you very much Chris, Xavier and ms (;) for your comments and I will take
into account your suggestions in my proposal (for GENCI, Chris ;)) .
A bientot
Stefane
--
Message: 1
Date: Thu, 14 Oct 2010 17:22:
On 2010-10-14 21.51, Jyoti Mahalik wrote:
Using g_energy I can extract the energy of the whole system. But I want
to extract the energy (potential energy) of the protein units in my
system. Is it possible to do it in GROMACS or any other application?
How would you define that?
--
David van der
Using g_energy I can extract the energy of the whole system. But I
want to extract the energy (potential energy) of the protein units in
my system. Is it possible to do it in GROMACS or any other application?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/l
On Oct 14, 2010, at 11:42 AM, ms wrote:
On 14/10/10 17:32, XAvier Periole wrote:
Then I am not a fan of implicit solvents so I'll pass on that, then
for the
coarse grained FF the OPEP FF seem to be fine for your application.
You can also look at the ones from Deserno's group (bereau-2009) a
On 14/10/10 17:32, XAvier Periole wrote:
Then I am not a fan of implicit solvents so I'll pass on that, then for the
coarse grained FF the OPEP FF seem to be fine for your application.
You can also look at the ones from Deserno's group (bereau-2009) and
from Feig's group (primo: gopal-2010). I a
Well indeed the more atoms (degrees of freedom) in your system the
more replicas you need to insure exchanges between temperatures ...
I would say that even 135 replicas * 16 cpus= 2160 cpus ... that is
still
an enormous amount of cpu time for 12 small peptides :))
do you need to go up to 60
Hi all,
Is there a trick in gromacs to exclude some particles from the
pressure calculation procedure? E.g. to get partial pressure(s)...
Thank you!
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
gmx-users mailing li
Stefane,
why are you hesitant to reduce the size of your system. If you can
still address the same questions with a smaller system, then I'd say
the answer is nearly always to use that smaller system (REMD or not).
Besides, my gut feeling is that even if you had enough 271*16 cpus
availab
Dear all,
I come back to you for several questions about the futures replica-exchange
calculations that i would like to perform. The system of interest will contain
12 peptides (with 7 residues each) and 4 water molecules, it come from a
previous MD performed in NPT ensemble. With these s
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Hash: SHA1
On 10/14/2010 04:41 PM, Eudes Fileti wrote:
> Dear Florian, thanks for the help. I wonder just one more thing.
> Is it possible to obtain the lateral diffusion coefficient in a specific
> plane (say xy)
> using g_velacc? Or it is only possible with g
Dear Florian, thanks for the help. I wonder just one more thing.
Is it possible to obtain the lateral diffusion coefficient in a specific
plane (say xy)
using g_velacc? Or it is only possible with g_msd?
Bests
eef
___
Eudes Eterno Fileti
Física da Matéria Condens
hey thanks Sander for bringing my attention to -nt option.. ;)
--
sikandar
On Thu, Oct 14, 2010 at 6:08 AM, Sander Pronk wrote:
>
> On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote:
>
> > Recently I installed gromacs4.5.1 without mpi support on my workstation
> with 8 cores using cmake and m
Dear Javier,
Thank you for you suggestions. I am looking into these things and for
sure take yours and Xavier's earlier comments into account.
Sincerely,
George
On 10/14/2010 3:57 AM, Javier Cerezo wrote:
Hello George.
I would inspect PG lipid head (in Tieleman's website) in order to
ext
Dear all,
to deal with my long-range interactions I used the reaction-field-zero
method. Therefore I searched for a publication of this method but did
not find a reference in the manual or on the gromacs website. Can
anybody tell me the publication on which the implemented reaction-field
is b
On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote:
On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote:
Hi gmx-users
I finished a series of pulling runs using the "periodic_direction"
option
and when I run the g_wham analysis I received the following message.
---
fancy2012 wrote:
Dear gmx users,
In gromacs-4.5.1, we can use amber force field now, but if I want to
gaff, a force field of small molecules, How should I do? Could someone
give me some suggestion?
If you have an AMBER topology, there are scripts on the GROMACS website to
convert it to the
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Hash: SHA1
On 10/14/2010 01:33 PM, Eudes Fileti wrote:
> Hi Florian, in fact I had already realized that it was possible
> to calculate the VACF without using the -m option (although this option
> was important for my calculations).
>
> I have not received any
Dear gmx users,
In gromacs-4.5.1, we can use amber force field now, but if I want to gaff, a
force field of small molecules, How should I do? Could someone give me some
suggestion?
Thanks in advance!
All the best,
fancy--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/m
Cenfeng Fu wrote:
Several possible reasons:
1. The force field parameters aren't perfect, so there is some inherent
disagreement between simulation and reality. What is the expected
value for
this force field?
2. You're using the isothermal compressibility for wat
Jennifer Williams wrote:
Hi,
So, I did as suggested. Ran PRODRG the first time using the JME Editor
and took the pdb file from this. Then I added the ADDHYD OAE underneath
(actually it doesn't matter which O (OAD or OAE) is protonated as long
as it is only one of them).
The first bit of
Hi,
So, I did as suggested. Ran PRODRG the first time using the JME Editor
and took the pdb file from this. Then I added the ADDHYD OAE
underneath (actually it doesn't matter which O (OAD or OAE) is
protonated as long as it is only one of them).
The first bit of output looked encouraging
mohsen ramezanpour wrote:
I am not sure.
How can I check it?
I think as you.but I don't know what and how can I modify it.
Look at the .log file for any indication of whether or not the job is still
running. Check the .edr and .xtc files with gmxcheck to see how many frames
they contain.
Hi Florian, in fact I had already realized that it was possible
to calculate the VACF without using the -m option (although this option
was important for my calculations).
I have not received any attachment, have you send me something?
If necessary, please, send it to my email.
Following your sug
ocourse my running took a few hours time.is it possible crashing?
On Thu, Oct 14, 2010 at 2:54 PM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> I am not sure.
> How can I check it?
> I think as you.but I don't know what and how can I modify it.
>
>
> On Thu, Oct 14, 2010 at 1:52 PM
I am not sure.
How can I check it?
I think as you.but I don't know what and how can I modify it.
On Thu, Oct 14, 2010 at 1:52 PM, ms wrote:
> On 14/10/10 08:51, mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I am running a seamulated anneaking + MD in my cluster.
>> I had done it for 2 times.
>>
On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote:
> Recently I installed gromacs4.5.1 without mpi support on my workstation with
> 8 cores using cmake and make -j 8, make install commands ( as suggested on
> installation instructions).
>
> Now when I do mdrun it automatically utilizes all t
You need to run PRODRG twice. The first time, do not use ADDHYD. Make note of
the atom names that PRODRG assigns. Then run PRODRG a second time, using ADDHYD
with the atom name that PRODRG uses for the O atom you want protonated.
-Justin
Jennifer Williams wrote:
Hi Justin,
Thanks for
Hi Justin,
Thanks for your answer. The ADDHYD in the FAQ sounds like exactly what
I need however I can't get this command to work. I draw in my molecule
using the JME editor and get this .pdb file in the PRODRG window.
CC(C)Cc1ccc(C(C)C(=O)O)cc1
JME 2002.05 Thu Oct 14 10:48:38 BST 2010
On 14/10/10 08:51, mohsen ramezanpour wrote:
Dear All
I am running a seamulated anneaking + MD in my cluster.
I had done it for 2 times.
but my results are not as i expect.
I have attached my md.mdp file for you,I don't know which part of it is
wrong.
what i like to result is to change tempretur
Thank you Justin,
you Perl script has been a great help!
Cheers,
Carla
On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul wrote:
>
> I wrote a Perl script to do a similar task (appended below). Perhaps it
> will be useful to you. I hope it works; I had to hack out some things that
> were spec
Dear all,
I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started to run
demo but still its running ( more then 5 hrs). How long will take time to
complete.
Any other possible way is there to increase speed ?
Anybody can help me?
Advance thanks
--
--
Regards,
N. Sathishkumar,
--
gm
Sorry, for the mistake: not Tieleman's website, but Martini's.
POPG, is an example for PG lipid. In that one, the OH-C-C-OH is
represented with a P4 particle as Xavier proposed.
Javier
El 14/10/10 09:57, Javier Cerezo escribió:
Hello George.
I would inspect PG lipid head (in Tieleman's webs
Hello George.
I would inspect PG lipid head (in Tieleman's website) in order to
extract the parameters for some groups, such as the "glicero-ester"
(atom name GL0 in the topology), and then take a particle for usually
used for esters such as "Na". Anyway, even that topology for Tieleman is
no
Dear All
I am running a seamulated anneaking + MD in my cluster.
I had done it for 2 times.
but my results are not as i expect.
I have attached my md.mdp file for you,I don't know which part of it is
wrong.
what i like to result is to change tempreture from 420 in 0 ps to 450 in 20
ps and then gra
Hi,
I think the PMF is something like PMF = kT ln[g(r)] where g(r) is the
radial distribution function from g_rdf.
Emu
>>> Sanku M 13.10.10 17.35 Uhr >>>
Hi,
I am studying Potential of mean force(PMF) of association of two peptides. I
want to decompose the PMF into energy(enthalpy)
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