Dear users,
I am performing MD simulations of short peptides (from 7 to 45 units) in
implicit solvent. I found quite bizarre results: all peptides unfold after
few picosends, adopting a rather linear conformation until the end of MD,
irrespective of temperature (I performed simulations at 200K,
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
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 system is a protein-ligand complex. Firstly, i run a minimization, and
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
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 implicit solvent is about 1.5ns per day.
With respect to the accuracy of
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
Dear,
there are three waters in active site of receptor,mediating the binding of
ligand with target protein. i want to study the three waters how to affect the
binding of ligand with target protein and the contribution to the stability of
the system.
In order to avoid the three waters
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
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 method. The question is - can I use imlicit
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 charmm27+cmap
forcefield. I am trying to use the
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
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 implicit
solvent. Otherwise one should use large
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
Dear all GROMACS users,
I would like to know if gromacs has implicit solvent model for GROMOS
force field or not? If it has, where is the model file (similar gbsa.itp
in some ff as amber, charm27 or OLPS FF)?
Thank you very much.
Yours sincerely,
MHViet
--
gmx-users mailing list
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
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 Interlandi, PhD
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
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Thanks!
--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See
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]
is a hammer, every problem begins to resemble a nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of liaoxyi
Sent: Wednesday, 12 October 2011 3:59 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Implicit solvent problems
Hi, dear all,
I'm doing
Hi, dear all,
I’m doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solvent model with
GMX4.5.3.
First, minimize. When doing this I got the result as below:
Step= 0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06,
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=
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 lysozyme). Running simulations with finite cutoffs
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
Dear GROMACS experts:
I'm using a GB implicit solvent function in ver. 4.5.4.
When I switched on GMX_NB_GENERIC with implicit_solvent=GBSA,
I've got the message,
Fatal error:
Death horror! GB generic interaction not implemented.
I'm wondering that is it difficult to add some code to
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?
Besides, what type of ensemble would be a good
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.
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) missing or negative for atom type 'H2'
GB
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:
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
mdrun, but soon after starting, mdrun complains about excessive rotation
in LINCS (see the error printed below that). I also include my mdp
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,
I have been tracking the code for implicit solvent,
i.e. src/mdlib/genborn.c
According to the gromacs paper on implicit solvent, J Comp Chem 31:2593,
2010, the GB force is tabulated in the X = Rij Ci Cj dimension.
However, the tabulated function, which I think is stored in fr-gbtab, is
only
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 everyone,
I am going through the source code for the GB calculation part of gromacs,
and found the following code in src/mdlib/genborn.c :
in the function real calc_gb_nonpolar()
rai = top-atomtypes.gb_radius[md-typeA[ai]];
rbi_inv = fr-invsqrta[ai];
rbi_inv2 = rbi_inv * rbi_inv;
tmp
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
I recently came across a paper (J. Phys. Chem. B 2005, 109,
10441-10448) in which the authors found that using implicit
solvent with explicit ions you easily end up with all the
ions cuddling up in clusters ... which is obviously an artefact.
That is, if you do use this combination you
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?
The simulation was run using GROMACS 4.5 with the amber96ff
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
Dear, all
I just begin to work in gromacs.
I would like to run on a protein with amber99.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).
In mdout.mdp
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
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.
Thanks,
Esteban
A repeating question on the mailing list whether GROMACS can perform
implicit solvent simulations. The answer is, not really. Over the
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...
Dear all:
I know this question has been asked many times, but it's still
tempting for me to ask it again ;-). Could any one suggest a mdp file,
including the proper parameter setting, for implicit solvent
simulation in gromacs? From all the clues I gathered (the roadmap, the
source
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.
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.
Does anyone know how to implement implicit solvent in the Concurrent version
system ?
Thanks
--
Milad Ekramnia
Physics Department
Isfahan University of Technology
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
Hi everyone!!!
Can I use implicit solvent in a MD simulations on gromacs?
How can I do it?
Thanks for your help!!!
Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000 ext. 2792
Universidad Industrial de
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
implicit solvent has apparently been implemented in the openMM
modification of gromacs, although that is still in beta and is not to
be trusted for production runs without doing your own testing. I have
not tried it myself.
You can obtain it here:
https://simtk.org/home/openmm
-- original
von deisy yurley rodriguez
sarmiento
Gesendet: Donnerstag, 21. Jänner 2010 17:12
An: Gromacs
Betreff: [gmx-users] Implicit Solvent
Hi everyone!!!
Can I use implicit solvent in a MD simulations on gromacs?
How can I do it?
Thanks for your help
*An:* Gromacs
*Betreff:* [gmx-users] Implicit Solvent
Hi everyone!!!
Can I use implicit solvent in a MD simulations on gromacs?
How can I do it?
Thanks for your help!!!
Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica
Hi,
Of previous discussions on the list and the wiki I conclude one can do
implicit solvent simulations in GROMACS with the latest git version, but
that for the moment it is rather slow. I would like to test something
and it is not really a problem that the code is slow. So I guess I could
use
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
minimization?
2. What minimum
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
Hi,
I was curious to know whether gromacs 4.0 supports implicit solvent
simulation or not. If not, is there any possibility that the implicit solvent
model will be implemented in near future ?
Thanks
Jagannath Mondal
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