Yes, this is probably caused by a known bug in 4.6 that has been fixed
for a month or two and mentioned in the release notes. Some
work-arounds are suggested here
http://redmine.gromacs.org/issues/1249, but you should probably update
to 4.6.3 :-)
Mark
On Wed, Jul 10, 2013 at 5:43 PM, Cristina
On Wed, Mar 27, 2013 at 9:27 AM, xiao helitr...@126.com wrote:
Dear Gromacs users:
I did a protein MD using implicit solvent and Amber 99SB force filed.
However, i found that the implicit solvent is not faster than explicit
solvent, and what is worse is that it is also not accurate.
The
On Wed, Mar 27, 2013 at 10:11 AM, xiao helitr...@126.com wrote:
Dear Justin,
Thank you very much for your reply.
I found that the speed of implict MD is slower that explict MD. For
examplex, the speed of an explict MD for a protein of 300 amino acids is
about 3ns per day, however, the
Dear Justin,
Thank you very much for your suggetions.
BW
Fugui
At 2013-03-27 22:15:23,Justin Lemkul jalem...@vt.edu wrote:
On Wed, Mar 27, 2013 at 10:11 AM, xiao helitr...@126.com wrote:
Dear Justin,
Thank you very much for your reply.
I found that the speed of implict MD is slower that
On 2/14/13 1:01 AM, Алексей Раевский wrote:
Hi, dear developers!
I want to ask you abou dynamics in implicit solvent. I have a complex of
animal protein - dimer/trimer. After modeling by homology I have built
another one from the plant organism. Dimer/trimer was constructed with
superposition
, your statement saying that :
you can only run on 1-2 processors in implicit solvent.
Thank you,
Sebastien
Date: Thu, 14 Feb 2013 08:03:28 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Implicit solvent
On 2/14/13 1:01 AM, Алексей Раевский wrote:
Hi, dear
On 2/14/13 10:21 AM, Sebastien Cote wrote:
Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born-formalism implemented in
GROMACS?
For the case of optimizing and relaxing a system (expecting short MD), I
-0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Implicit solvent
On 2/14/13 10:21 AM, Sebastien Cote wrote:
Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born
On 2/14/13 11:02 AM, Sebastien Cote wrote:
Dear Justin,
Thank you very much for your answer.
I did not take this as a criticism of implicit solvent model. I was just
wondering what was the origin of the limitations you were speaking of.
I did some small implicit solvent simulations, but I
On 14/08/2012 1:07 AM, Sai Pooja wrote:
Hi,
I have read a couple of posts on related topics but I am still not
sure how to proceed and would be grateful to get some help.
I want to run implicit solvent simulations of a protein+water
(implicit) system in the canonical ensemble using
On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote:
Dear all,
I know several questions about implict solvent have already been asked in this
list. I think and hope the question I have has not been raised. Forgive me if I
am wrong.
I have read that all-to-all kernels are the best option when doing
On 07/03/2012 11:01 PM, Justin A. Lemkul wrote:
On 7/3/12 8:57 AM, Ramon Crehuet Simon wrote:
Dear all,
I know several questions about implict solvent have already been
asked in this list. I think and hope the question I have has not been
raised. Forgive me if I am wrong.
I have read that
On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
I run energy minimization of my protein with implicit
On 29/02/2012 9:26 PM, Steven Neumann wrote:
On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
hi steven,
i've been simulating a 33 AA peptide for the past two days using
implicent solvent in order to achieve a proper folding.
i haven't added counterions, however, the systems shows nice results
according to what i've expected. the mdrun command (for the extension)
for our hardware
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Steven
On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz dur...@zib.de wrote:
hi steven,
i've been simulating a 33 AA peptide for the past two days using implicent
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann s.neuman...@gmail.com wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of LINCS warning.
Also thanks Vedat
lina wrote:
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann s.neuman...@gmail.com wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of LINCS warning.
A
Thank you all!
How about -DFLEXIBLE in both em and md?
Steven
On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
actually, as far as i know, the -DFLEXIBLE argument has no effect on
simulations without explicit water ?!
i just copied the define line from my explicit simulation systems ..
so, the only define value, that has a meaning is -DPOSRESHELIX.
i didn't use constraints for the first time in my
Vedat Durmaz wrote:
actually, as far as i know, the -DFLEXIBLE argument has no effect on
simulations without explicit water ?!
The #ifdef FLEXIBLE block does only affect explicit water, unless the topology
is somehow modified to use this type of term (probably not). It shouldn't be
thanks justin for clearing up these issues ..
Am 28.02.2012 15:50, schrieb Justin A. Lemkul:
Vedat Durmaz wrote:
actually, as far as i know, the -DFLEXIBLE argument has no effect
on simulations without explicit water ?!
The #ifdef FLEXIBLE block does only affect explicit water,
I run energy minimization of my protein with implicit solvent:
constraints = none
integrator = steep
dt = 0.001 ; ps
nsteps = 3
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all (no cut-off),
which gets
Steven Neumann wrote:
I run energy minimization of my protein with implicit solvent:
constraints = none
integrator = steep
dt = 0.001 ; ps
nsteps = 3
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0
hi jan/steven (?),
you should know, in contrast to let's say justin lemkul, i haven't that
much experience with molecular simulations!
actually, i don't expect large differences in conformational/statistical
properties depending on the usage of lincs constraints. usually i use
them when
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
I run energy minimization of my protein with implicit solvent:
constraints = none
integrator = steep
dt = 0.001 ; ps
nsteps = 3
vdwtype = cut-off
coulombtype =
Thank you Vedat!!!
On Tue, Feb 28, 2012 at 8:35 PM, vedat durmaz dur...@zib.de wrote:
**
hi jan/steven (?),
you should know, in contrast to let's say justin lemkul, i haven't that
much experience with molecular simulations!
actually, i don't expect large differences in
On 29/02/2012 1:11 AM, lina wrote:
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumanns.neuman...@gmail.com wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of
Steven Neumann wrote:
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
I run energy minimization of my protein with implicit solvent:
constraints = none
integrator = steep
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using a GBSA method. Is it compatible with the CHARMM22 force field?
look for gbsa.itp showed
lina wrote:
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using a GBSA method. Is it compatible with the CHARMM22 force field?
look for gbsa.itp
On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using a
On 23/01/2012 1:01 PM, Gianluca Interlandi wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit
solvent model using a GBSA method. Is it compatible with the CHARMM22
force field?
Thanks,
Gianluca
Gianluca Santoni wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
http://www.gromacs.org/Documentation/Tutorials
If it's not there, or Google can't find it, the answer is no.
-Justin
--
Justin A. Lemkul
Ph.D.
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
gianluca.sant...@ibs.fr wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1] pdb2gmx the water model choose none.
2] after editconf, go to energy minimization directly
* It's
lina wrote:
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
gianluca.sant...@ibs.fr wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1] pdb2gmx the water model choose none.
2] after editconf, go to energy minimization
On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
gianluca.sant...@ibs.fr wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1]
Did you look at atom 2073?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is
On 12/10/2011 3:59 PM, liaoxyi wrote:
Hi, dear all,
I'm doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solventmodel with
GMX4.5.3.
First, minimize. When doing this I got the result as below:
Step=0, Dmax= 1.0e-02 nm, Epot=
On 12/07/2011 4:51 AM, Justin A. Lemkul wrote:
Hi All,
I'm having a strange problem with some implicit solvent systems and
I'm wondering if anyone's experienced the same problem or if I've
stumbled upon a bug. I'm testing some methodology with a robust
system (everyone's favorite, 1AKI
Mark Abraham wrote:
On 12/07/2011 4:51 AM, Justin A. Lemkul wrote:
Hi All,
I'm having a strange problem with some implicit solvent systems and
I'm wondering if anyone's experienced the same problem or if I've
stumbled upon a bug. I'm testing some methodology with a robust
system
E. Nihal Korkmaz wrote:
Dear all,
This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp
I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Not usually.
On 16/06/2011 7:59 PM, Netaly Khazanov wrote:
Hi,
My system is protein +DNA.
I am trying to perform implicit solvent calculation using Amber 99.
In the begging I wanted to minimize the system and got this error message.
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s)
Scratch what I said last night about pressure coupling - it crashes
after ~200K timesteps due to fluctuations in the cell volume. I'm
sticking with NVT for now.
On 5/31/2011 6:14 PM, Michael Daily wrote:
The following mdp file produces a successful dynamics run out to 100K
steps / 200 ps.
This isn't surprising. Pressure coupling without explicit solvent
doesn't work the way that you are anticipating. You might want to look
at what happened to the system using ngmx or VMD to see what went wrong.
Unless you need to simulate in a box for some reason, you should turn
off PBC as Justin
The following mdp file produces a successful dynamics run out to 100K
steps / 200 ps. What I discovered is this:
Using the md integrator, it is necessary to turn off pressure coupling.
However, pressure coupling works with sd (Langevin) integrator.
Mike
---
; title and include files
Thanks for the suggestions. I can see how a smaller dt would probably be
the most general approach to use as it should work with just about any
reasonable combination of settings.
-- Josh
On Tue, 2011-05-31 at 11:02 +1000, Mark Abraham wrote:
On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:
Michael D. Daily wrote:
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with the
charmm forcefield. I am able to minimize successfully and compile for
When troubleshooting, it is always advisable to try the latest version (4.5.4)
to see if the problem is
Thanks Justin, this is very helpful. I'll attempt these fixes tomorrow.
Mike
On 5/30/2011 5:50 PM, Justin A. Lemkul wrote:
Michael D. Daily wrote:
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with
the charmm forcefield. I am able to minimize successfully and
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of explicit water) allows the protein to change conformation much faster
than LINCS
Joshua L. Phillips wrote:
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of explicit water) allows the protein to change
On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:
Joshua L. Phillips wrote:
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of
Thanks for the recommendations everyone. I tried all of the mdp changes
recommended by Justin (increase rlist, rvdw, etc to 2.0; change
T-coupling to v-scale, and eliminate P-coupling). When I increased the
distance cutoffs, it ran about 30 ps then crashed instead of crashing
immediately.
Hi!
The tabulated function is applied to all interactions, both bonded and
non-bonded. The function is initialized in make_gb_table(), and accessed in the
non-bonded kernels the same way as other tabulated functions are accessed. See
GBtab[nnn] in the kernels for more details.
In
Hi!
I know about this difference. The only reason for it is that, when I first
started with this I used Tinker as a reference implementation, which has the
6-th power in the code.
The differences should be small, though. The non-polar part only amounts to a
few percent of the total force
Andrew Mauro wrote:
Hi,
While running a simulation of capped alanine in an implicit solvent the
molecule appears to collapse on itself such that the atoms have
coordinates of 0,0,0 or some even have NaN. Has anyone else had this
problem or any suggestions?
Sounds like
Hi!
Starting an implicit solvent simulation works just as starting a normal,
explicit solvent simulation, except there is no solvent molecules.
You should use version 4.5.3 for this though (4.0.5 will not work).
Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
grompp,
Thanks!
If I understand you correctly, I need to do this (?):
1.
pdb2gmx
2.
Adding ions (if I have no SOL, what is better to choose on this step?)
3.
Minimization with mdp file, that includes these lines:
implicit_solvent = GBSA
gb_algorithm = {Still,HCT,OBC}
Thanks again!
Don't you know how to make a total charge = 0 in this case, if implicit salt
concentration is not implemented currently? Or it is not critically?
2011/3/10 Per Larsson per.lars...@sbc.su.se
Hi!
Yes, except that in point 2, I'm not sure about the effects of explicit
ions in an
Hi!
The answer is that I do not now critical it is.
I have seen some papers that seem to hint at it not being overly critical, but,
again, life does not come at a net charge.
You'd have to see for yourself in your system, given the observables that are
important I suppose.
Possibly we can
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
-Justin
Thanks,
Esteban
A repeating question on the mailing list
On 05/07/10 16:27, Justin A. Lemkul wrote:
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
Since it interests me too...
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
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.
deisy yurley rodriguez sarmiento wrote:
Hi everyone!!!
Can I use implicit solvent in a MD simulations on gromacs?
How can I do it?
Thanks for your help!!!
Implicit solvent simulations will be supported when Gromacs 4.1 is released.
-Justin
Deisy Y. Rodriguez S.
Practicante de Computos
Grace Tang wrote:
Hello All,
I am doing energy minimization on a protein crystal structure to relax
it. Afterwards, I plan to run md simulation with implicit solvent. I
am new at this and have many questions.
1. Should the implicit solvent conditions be enabled when I run the
energy
Sorry, I wasn't too clear in the first message. I will be using OpenMM
Gromacs, which does support implicit solvent. My current energy
minimization steps only lower the energy to -5E3. Is this okay considering
water is not around?
Is is necessary to do equilibration if I am using implicit
Grace Tang wrote:
Sorry, I wasn't too clear in the first message. I will be using OpenMM
Gromacs, which does support implicit solvent.
My current energy minimization steps only lower the energy to -5E3. Is
this okay considering water is not around?
Probably.
Is is necessary to do
On Fri, 19 Sep 2008 17:28:20 +0530 (IST)
Anirban Ghosh [EMAIL PROTECTED] wrote:
Hi All,
I am simulating a Coarse Grained model using implicit solvent condition. Can
Periodic Boundary Condition and Particle-Mesh-Ewald be used with implicit
solvent simulation?
What would be the use of PME
Hi,
The same as in normal simulations.
I always use PME and PBC in my implicit solvent simulations.
Berk
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 14:52:39 +0200
On Fri, 19 Sep 2008 17:28:20 +0530 (IST
Simulation of a crystal in implicit solvent?
Tsjerk
On Fri, Sep 19, 2008 at 2:52 PM, Xavier Periole [EMAIL PROTECTED] wrote:
On Fri, 19 Sep 2008 17:28:20 +0530 (IST)
Anirban Ghosh [EMAIL PROTECTED] wrote:
Hi All,
I am simulating a Coarse Grained model using implicit solvent condition.
in implicit solvent?
I really do not see the point!
Tsjerk might have a point with crystal packing ...
Berk
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 14:52:39 +0200
On Fri, 19 Sep 2008 17:28:20 +0530 (IST)
Anirban
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 16:42:15 +0200
On Fri, 19 Sep 2008 15:00:18 +0200
Berk Hess [EMAIL PROTECTED] wrote:
Hi,
The same as in normal simulations.
I always use PME and PBC in my
Hi,
Having a non-uniform dielectric permittivity is a non-trivial problem to solve.
I would like to have a solver for such electrostatics in Gromacs,
but it is a lot of work to implement (and to make it efficient).
Reaction field does not do anything for you in this respect.
Berk
From: [EMAIL
On Fri, 19 Sep 2008 16:49:45 +0200
Berk Hess [EMAIL PROTECTED] wrote:
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 16:42:15 +0200
On Fri, 19 Sep 2008 15:00:18 +0200
Berk Hess [EMAIL PROTECTED] wrote:
Hi
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 17:03:08 +0200
On Fri, 19 Sep 2008 16:49:45 +0200
Berk Hess [EMAIL PROTECTED] wrote:
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit
On Fri, 19 Sep 2008 17:25:41 +0200
Berk Hess [EMAIL PROTECTED] wrote:
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent PBC
To: gmx-users@gromacs.org
Date: Fri, 19 Sep 2008 17:03:08 +0200
On Fri, 19 Sep 2008 16:49:45 +0200
Berk Hess [EMAIL PROTECTED] wrote
Hello Una (and everyone else)
I'm happy to announce that, while not yet available in cvs, it will
very soon be possible to do implicit solvation with Gromacs.
I'm have a working implementation almost finished, and are currently
running some tests to assure that the code is stable.
With any
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
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):
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
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
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
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=pubmedpubmedid=15814616
Tom
--On Wednesday, July
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
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
: [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,
however, isn't
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
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
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
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 priorities I
[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
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
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
Dmitriy Golubobsky wrote:
Hi,
i've got a question: is it possible to compute implicit solvent in gromacs?
no
i'd like to change dielectric constant, and use
*Generalized-Reaction-Field for modeling my polymer.*
--
Dmitriy Golubovsky
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