Implicit solvent are still not available in gromacs.
Using 43a1 FF is fine, except with implicit solvent! Or you should
have one compatible with it!
On Apr 28, 2010, at 6:27 PM, Chanchal wrote:
Hi All,
I want to perform MD simulation of a protein in implicit solvent
using gromacs 4.0.7. I
Chanchal wrote:
Hi All,
I want to perform MD simulation of a protein in implicit solvent using
gromacs 4.0.7. I looked into the manual but did not get any information
regarding the implicit solvent. Is it avilable in gromacs? I searched in
the mailing list and found someone in older mail s
Hi All,
I want to perform MD simulation of a protein in implicit solvent using
gromacs 4.0.7. I looked into the manual but did not get any information
regarding the implicit solvent. Is it avilable in gromacs? I searched in the
mailing list and found someone in older mail said its not avilable. I
Hi,
On Jul 19, 2007, at 10:15 AM, Edgar Luttmann wrote:
I can't find any usage of the GB parameters as read from the mdp
file - neither in the latest release nor the HEAD revision in the
CVS. Is there another branch in the CVS you got that code in?
No, at least not publicly available atm.
Although I realize it is the holiday season, at least in Europe, I
would like to once more recommend the development wiki for
documenting this kind of discussion, and for publishing
specifications for algorithms, like (totally unrelated, but came up
earlier today):
http://wiki.gromacs.
Hi Erik,
Erik Lindahl wrote:
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs. Rather,
Erik Lindahl started the implementation of this stuff but did never
finish it completely, due to other priorities I presume. We shoul
There is a niche for implicit solvent if you need to do more
extensive conformational sampling than you can achieve with
atomically detailed solvent---and if you can plausibly argue that you
are not introducing such egregious systematic errors that you are
just sampling more junk.
At 09:23 AM
[EMAIL PROTECTED] wrote:
Selon Erik Lindahl <[EMAIL PROTECTED]>:
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to
Selon Erik Lindahl <[EMAIL PROTECTED]>:
> Hi,
>
> On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
>
> > The version used by Alan Mark has never made it into gromacs.
> > Rather, Erik Lindahl started the implementation of this stuff but
> > did never finish it completely, due to other prior
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to other priorities I presume.
We should however take out the vari
Stéphane Téletchéa wrote:
Moore, Jonathan (J) a écrit :
I asked for and received the code a couple of years ago.
As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges. Also, the different models (Still, etc.) are
implemented in independent versions of the cod
Moore, Jonathan (J) a écrit :
I asked for and received the code a couple of years ago.
As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges. Also, the different models (Still, etc.) are
implemented in independent versions of the code. Also, the GB part is
ac
l Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ran Friedman
Sent: Wednesday, July 18, 2007 10:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Implicit solvent simulation
Dear Tom,
The paper is available and was mentioned in the list. The model,
howev
If you REALLY want implicit solvent then i suggest you contact the authors
and ask them about it, however i (like most others i think) have never
needed to use implicit solvent.
Tom
--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman
<[EMAIL PROTECTED]> wrote:
Dear Tom,
The paper is
Dear Tom,
The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.
Ran.
TJ Piggot wrote:
> Hi,
>
> Just to let people know in case they are unaware there is a paper
> where implicit solvent models have been implemented in GROMACS, the
> paper can be found
Hi,
Just to let people know in case they are unaware there is a paper where
implicit solvent models have been implemented in GROMACS, the paper can be
found using the following link:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15814616
Tom
--On Wednesday, July 1
SeungPyo Hong wrote:
Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.
I've put it on the development TODO list (feel free to volunteer)
http://wiki.gromacs.org/index.php/Implicit_Solvent
The reason it is not t
Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not implemented
in Gromacs.
Sincerely,
Seungpyo Hong
On 7/16/07, Stéphane Téletchéa <[EMAIL PROTECTED]> wrote:
SeungPyo Hong a écrit :
> Dear gmx-users,
>
> Recently I want to perform MD for p
SeungPyo Hong a écrit :
Dear gmx-users,
Recently I want to perform MD for protein with implicit solvent model.
Gromacs does not seem to support it.
Could you let me know where to find information about implicit solvent
simulation with Gromacs?
Also I will be glad if you tell me your opinion abo
Dear gmx-users,
Recently I want to perform MD for protein with implicit solvent model.
Gromacs does not seem to support it.
Could you let me know where to find information about implicit solvent
simulation with Gromacs?
Also I will be glad if you tell me your opinion about the implicit solvent
si
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