Hello all,
I am trying to test the martini force field with PME for a charged system that
contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My
system works well, if i use the standard shift parameters (correct temp, and
pressure). But for for the simulation with PME ,
Did you visualise the system? T in function of time? Epot in function of time?
As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist =
1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if
nstlist =10.
On Apr 25, 2013, at 1:10 PM, ABEL Stephane
Hmmm
Aren't the keywords here charged system + PME?
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:
Did you visualise the system? T in function of time? Epot in function of
time?
As a side note (not relevant for PME) the mix of nstlist = 10
also visualized my system at the end of the NPT run, the na+, water,
surfactant, octane molecules form a slab with void
What's wrong ?
Stephane
--
Message: 5
Date: Thu, 25 Apr 2013 13:34:21 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users
-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl
Content-Type: text/plain; charset=us-ascii
Did you visualise the system? T in function of time? Epot in function of time?
As a side note
And ? sorry but i do not understand...
Stephane
--
Message: 2
Date: Thu, 25 Apr 2013 15:39:12 +0200
From: Dr. Vitaly Chaban vvcha...@gmail.com
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message
. Vitaly Chaban vvcha...@gmail.com
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAPXdD+bDiuQWG_3eWZ_0yb=
aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hmmm
vvcha...@gmail.com
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAPXdD+bDiuQWG_3eWZ_0yb=
aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hmmm
Aren't the keywords
Thanks Justin.
The help has been much appreciated.
Cheers,
Davide
On 7/02/13 8:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/7/13 2:29 PM, Davide Mercadante wrote:
Thank you Justin,
I guess this means that this kind of simulations is not possible
without a
modification of the
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.
After the equilibration I start a
On 2/7/13 5:20 AM, Davide Mercadante wrote:
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a simulated
time where the pull
On 2/7/13 1:44 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
Thanks.
Cheers,
Davide
On 7/02/13 8:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/7/13 1:44
On 2/7/13 2:29 PM, Davide Mercadante wrote:
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
If you're looking to unfold secondary structure
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force field. Every force
field is different and requires proper settings.
-Justin
--
Thank Justin !
On Tue, Dec 18, 2012 at 10:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force
On 10/12/12 10:42 AM, rama david wrote:
Hi Gromacs friends,
I planed to use martini coarse grained ff to my simulation protocol.
My simulation protocol is:
I am placing two peptide at far distance.IAt these point i am using Gromos
FF they are initially in random coil structure.
Now when I
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find them easily in the literature. Notably the ones from
Deserno or Derreumaux.
On Oct 10, 2012, at 2:03 PM, rama david wrote:
Hi friends,
I planed to use the martini force-field for my simulation study
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote:
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find
Nope, but on other softwares.
On Oct 10, 2012, at 2:50 PM, rama david wrote:
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl
wrote:
Martini
Hi thank you
Please told me the name of Freely available software on which these FF can
be used ..
Thank you in advance
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole x.peri...@rug.nl wrote:
Nope, but on other softwares.
On Oct 10, 2012, at
Hi rama,
actually MARTINI has been further improved to allow secondary structure
change.
The title is:
*Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model:
Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides*
and here there is a link to the paper:
No, it does NOT!
HAve you red the paper?!
This implementation is an adoc representation to mimic specific
sequences of short peptides! They do never for any secondary structure!
On Oct 10, 2012, at 3:05 PM, francesco oteri wrote:
Hi rama,
actually MARTINI has been further improved to
Well ... it always depends on what you want to do but the file on the
link you give are the official website and they should be reliable :))
On Oct 9, 2012, at 12:04 PM, rama david wrote:
Hi Gromacs friends,
I am interested in Martini force-field and application in lipid
bilayer.
I
Have you checked MARTINI website?
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
Dariush
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA
Hi Dariush,
I've checked but it seems there no parameters for my detergent.
Actully there are parameters for the polar head and the lipidic tail, so it
is worth trying to merge them
to have the correct representation!
Francesco
2012/5/21 Dariush Mohammadyani d.mohammady...@gmail.com
Have you
Sure, this is the way to make forcefield for your molecule. Also, please
check literature.
Good luck,
Dariush
On Mon, May 21, 2012 at 9:26 AM, francesco oteri
francesco.ot...@gmail.comwrote:
Hi Dariush,
I've checked but it seems there no parameters for my detergent.
Actully there are
Thee are not yet parameters for DDM but indeed the parameters for both
the head and the tail are defined separately. It would be very useful
to combine them and start building a detergent parameter library ...
the topologies would have to be tested against experimental and/or
atomistic
Dear gromacs users,
does someone of you know whether parameters for the detergent
dodecyl-beta-maltoside
are avalaible in MARTINI forcefield?
Thank you in advance,
Francesco
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the
I have a fully fluorinated alkane, and am wondering how to choose the right
atom-to-bead mapping. 4 CH2 groups form a C1 bead in Martini. Will CF2-CF2
(6 heavy atoms), also map to a C1 bead type? How does one go about making
the right choice?
Any suggestions will be so welcome
--
Maria G.
Dear GROMACS Specialists,
I have doubt about definition of tiofen ring in MARTINI CG force field. May I
ask you to help me, Please?
I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it
right?
Or should I change SC5 to C-S-C for .gro file?
And my definition of tiofen in
Where did you find the topology?
On Apr 10, 2012, at 10:44 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have doubt about definition of tiofen ring in MARTINI CG force
field. May I ask you to help me, Please?
I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-
C. Is it
@gromacs.org
Sent: Tuesday, April 10, 2012 5:16 PM
Subject: Re: [gmx-users] martini coarse-grained
Where did you find the topology?
On Apr 10, 2012, at 10:44 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have doubt about definition of tiofen ring in MARTINI CG force field. May I
ask you
: XAvier Periole x.peri...@rug.nl
To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Tuesday, April 10, 2012 5:16 PM
Subject: Re: [gmx-users] martini coarse-grained
Where did you find the topology?
On Apr 10, 2012, at 10:44 AM, dina dusti wrote
Subject: Re: [gmx-users] martini coarse-grained
Hi Dina,
Thiophen is a five-membered ring, like the histidine side-chain, which
is modeled with three beads. And then you ought to choose the bead
types such that they give good agreement with atomistic PMFs and/or
partitioning of the same compound
Dear Gromacs Specialists,
May I ask you to help me for definition of pyrrole, tiofen and aniline in
MARTINI coarse-grained force field, Please?
I defined them as following:
aniline (one benzene ring+NH2) = SC4, SC4, SNd
pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1
SC5 does not work?
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
On Thu, Mar 8, 2012 at 2:34 PM, dina dusti dinadu...@yahoo.com wrote:
Dear
: [gmx-users] Martini
SC5 does not work?
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
On Thu, Mar 8, 2012 at 2:34 PM, dina dusti dinadu
Mohammadyani d.mohammady...@gmail.com
*To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
*Sent:* Thursday, March 8, 2012 11:24 PM
*Subject:* Re: [gmx-users] Martini
SC5 does not work?
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department
From: Dariush Mohammadyani d.mohammady...@gmail.com
To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Thursday, March 8, 2012 11:24 PM
Subject: Re: [gmx-users] Martini
SC5 does not work?
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department
Dear all,
I am using martini force field to generate elastic network for my
protein. I generate a list of distance between all beads within a certain
distance by:
genrestr -f ***.gro -n index.ndx -constr -o constraints
getting the constraints.itp file and will continue
The website has been updated to fit a CG tutorial starting monday in
Lausanne.
The manner of the construction you describe in your email is not the
proper way to do it!
The new script is doing it properly.
If you want the old script to only generate the elastic network (as it
seems
Of XAvier Periole [x.peri...@rug.nl]
Sent: Friday, October 14, 2011 11:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Martini force field: elastic network
The website has been updated to fit a CG tutorial starting monday in
Lausanne.
The manner of the construction you
Subject: Re: [gmx-users] Martini force field: elastic network
The website has been updated to fit a CG tutorial starting monday in
Lausanne. The manner of the c...
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
for GROMACS users
Subject: Re: RE: [gmx-users] Martini force field: elastic network
Hi Hualin,
The elastic network should work; the help should be updated...
Note that only the 'elnedyn' method has really been tested.
Cheers,
Tsjerk
On Oct 14, 2011 7:11 PM, Li, Hualin
hualin
Thanks Justin and Thomas for the helpful comments. Thomas pointed to the
example I had in mind. I should have been more specific.
It is obvious that we should make the mapping of molecules more easily
accessible.
Tks for the comments,
XAvier.
On Aug 30, 2011, at 20:16, Thomas Piggot
it must be some example of mapping lipids on the website: cgmartini.nl
On Aug 30, 2011, at 3:55 AM, Michael Daily wrote:
Hi all,
I am trying to reverse-map some martini lipids to united atom. In
order to do this, I'd prefer to have an EXACT definition of the aa-
to-cg mapping. I cannot
Xavier,
I did find the atom2cg.awk script on the downloads- tools of the martini
website, but there is no corresponding one for lipids. In any case I can
probably figure out the mapping by trial and error, just based on inter-bead
distances, but it would be nice to have it officially documented.
Michael Daily wrote:
Xavier,
I did find the atom2cg.awk script on the downloads- tools of the
martini website, but there is no corresponding one for lipids. In any
case I can probably figure out the mapping by trial and error, just
based on inter-bead distances, but it would be nice to
Hi Mike,
If you download the rev_trans.tar.gz archive from the reverse
transformation tutorial on the Martini website
(http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation)
the mapping section at the end of the dppc.itp file provides the details
of the mapping for this
Hi all,
I am trying to reverse-map some martini lipids to united atom. In order to
do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I
cannot find this, only an imprecise graphic, in the MARTINI paper; the
martini.itp file doesn't appear to list which heavy atoms are
Dear users,
I was wondering if there is Martini topology available for simple formyl
(or aldehyde) group H - C = O. I would appreciate if somebody can direct
me to the place where such force field parameters are discussed.
Thanks,
George
--
George Khelashvili, Ph.D.
Department of Physiology
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
noted
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
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
Dear users,
I am trying to build Martini topology for monoolein molecule (I assume
that no such topology exists at this moment). It is obvious that the
tail part of the molecule is similar to DOPC lipid tail, however I am
not sure how to parametrize the head-group of monoolein. I would
Have you considered reading the few papers describing the
principle of parameterization with the Martini FF? There are basic
recipes described and specific applications detailed.
Looking at cgmartini.nl might also help you getting more information and
reach people involved in Martini
Dear Xavier,
I think I have figured out how to deal with the missing part. My problem
was OH-C-C-OH construct which is the headgroup of monoolein. After some
research, it looks like that it is parameterized based on ethanediol and
has P4 type. The rest of the molecule I guess should be
I do not know what is the structure of monoolein :((
Then it is strongly possible that OH-C-C-OH is best represented
by the P4 particle type. But it might not be that simple :))
you should once your (first) topology made try it out and compare
to as much data you can find ... experimental and
Hi all,
Can anyone provide me with the MARTINI parameters for graphenes/nanotubes ?
I read a few papers on that but parameters are missing.
Also are you aware of any program/tool to parametrize new molecules in
MARTINI or GROMACS?
Thanks,
Umesh
--
gmx-users mailing list
Umesh Ghoshdastider wrote:
Hi all,
Can anyone provide me with the MARTINI parameters for
graphenes/nanotubes ? I read a few papers on that but parameters are
missing.
Your best bet would be to contact the authors of those papers directly.
Also are you aware of any program/tool to
I am trying to set up a simulation of a protein with the MARTINI force field.
Two of the histidines in the protein are judged to be protonated and
thus charged. This histidine is not described in the MARTINI force
field as far as I can tell?
I thought I could modify my way out of it by
I am trying to set up a simulation of a protein with the MARTINI
force field.
Two of the histidines in the protein are judged to be protonated and
thus charged. This histidine is not described in the MARTINI force
field as far as I can tell?
No there is no parameters for charged
Hi,
It is better you plan this question in MARtini forum, there are experts that
can answer this question!
Please register in:
http://md.chem.rug.nl/cgmartini/index.php/user-platform/login
Rasoul
On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter
emanuel.pe...@chemie.uni-regensburg.de wrote:
Dears,
the MARTINI CG force field web site has been remodeled.
It now includes FAQs, tutorials, a forum and much more ...
http://md.chem.rug.nl/cgmartini
Enjoy.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
I wish G96 force fields had a similar website with so much useful
information.
It would be good if authors posted anything on the forum cause it's
completely empty right now.
2010/1/26 XAvier Periole x.peri...@rug.nl
Dears,
the MARTINI CG force field web site has been remodeled.
It now
So lets say that I delete the first frame from the trajectory in which some
atoms might have been outside the box. Everything should be within the box
once the simulation starts (from the second frame onwards)? So the procedure
should work if the reference structure is the second frame? I have
Lets make it clear. I can not tell you if the atoms in the second
frame are in the
box or not! You have to visualize it!
Honestly it is not in the first frame I can not see how it would in
the second!
You have to build a reference structure that has the bilayer in one
piece, then
the
For quite a long time I had the feeling that trjconv doesn't resolve all
situations. Following the very recent discussion between Roland Schutz
and Tsjerk, I'm not sure there is an immediate solution. Ad hoc
approaches such as preparation of tpr files from intermediate snapshots
were useful for me
Hello
I get this error while running Martini:
A list of missing interactions:
G96Angle of 1280 missing 1
Molecule type 'DUPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms356 global 135 137 138
Does this mean
I think the text below Fatal error: explains pretty clearly why this
interaction is missing.
Berk
Date: Fri, 25 Sep 2009 13:04:28 +0200
From: mariagorano...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] martini simulation problem with unsaturated lipid
Hello
I get this error while
--
Date: Wed, 2 Sep 2009 17:21:46 +0200
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
From: mariagorano...@gmail.com
To: gmx-users@gromacs.org
I will change the tau_p values, and report back. This might take more
I meant 3 instead of 30 ps.
I would say 1 ps is too short for systems with a phase with large molecules___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but
the bilayer drifted towards the edge of the box along the bilayer normal,
and eventually some of the
maria goranovic wrote:
Dear Experts
I had posted this earlier, but the problem was not solved by earlier
suggestions. So am posting again.
I am simulating a POPC bilayer using MARTINI. The simulation ran fine,
but the bilayer drifted towards the edge of the box along the bilayer
normal,
I am not sure how to fix the trajectory that has drifted ...
But if your bilayer drifts even if you use a removal of the COM for
the water and
bilayer separately that means there is problem in the code! And this
should be
fixed.
XAvier.
On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
I will try centering with one of the lipid tail atoms .. that could solve
the problem.
This the way I have specified the comm_groups:
nstcomm = 1
comm-grps = Lipid W
OR
nstcom = 1
comm-grps = system
-Maria
On Wed, Sep 2, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote:
I am not
Hi,
I am 99.99% sure that there is no problem with COM motion removal in Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory
so that the bilayer is at the center
lincs_warnangle = 30
On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote:
Hi,
I am 99.99% sure that there is no problem with COM motion removal in
Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users
post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so that the bilayer is at the center
Date: Wed, 2 Sep 2009 16:04:39 +0200
I am not sure how to fix the trajectory that has
...@hotmail.com wrote:
Hi,
I am 99.99% sure that there is no problem with COM motion removal in
Gromacs.
Could you post your mdp parameters?
Berk
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so
+0200
Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory
so that the bilayer is at the center
From: mariagorano...@gmail.com
To: gmx-users@gromacs.org
Oh dear. That is not good. the missing decimal point in tau_p it is a typo all
right. but it seems i have used
cause problems in single precision we should be aware
of this.
Could you report back if changing tau_p solves the drifting problem?
Berk
--
Date: Wed, 2 Sep 2009 17:06:50 +0200
Subject: Re: [gmx-users] Martini simulation problem in recentering
trajectory so
we did not manage to find the source
of this problem.
Thus it would be useful to see if a shorter tau_p fixes it in your case.
Berk
Date: Wed, 2 Sep 2009 17:21:46 +0200
Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory
so that the bilayer is at the center
From
Could you download this with another bowser?
On Feb 11, 2009, at 5:22 AM, weixin wrote:
Oh, sorry.
I mean the browser. (IE= internet explorer)
2009/2/10 XAvier Periole x.peri...@rug.nl
On Feb 10, 2009, at 9:54 AM, weixin wrote:
It's caused by the IE.
what is IE ?
2009/2/10 xi
I had the same problem with Internet explorer. Try Firefox!
Andrei
On Tue, Feb 10, 2009 at 9:41 AM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote:
well.. it seems that there is a problem in the page for downloading files
from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model
It's caused by the IE.
2009/2/10 xi zhao zhaoxiitc2...@yahoo.com.cn
well.. it seems that there is a problem in the page for downloading files
from
http://md.chem.rug.nl/~marrink/MARTINI/Parameters.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Parameters.html,
the cg model parameters can
On Feb 10, 2009, at 9:54 AM, weixin wrote:
It's caused by the IE.
what is IE ?
2009/2/10 xi zhao zhaoxiitc2...@yahoo.com.cn
well.. it seems that there is a problem in the page for downloading
files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html,
the cg model parameters
On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote:
-No: is where you can find much more arguments. First of all the two force
fields have not
been parametrized consistently. Second you'll probalby have problems in
defining the
interactions between the two approches. How
On Feb 3, 2009, at 4:03 PM, Elton Carvalho wrote:
On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole x.peri...@rug.nl
wrote:
-No: is where you can find much more arguments. First of all the
two force
fields have not
been parametrized consistently. Second you'll probalby have
problems in
Am I wrong, or are you considering some kind of MSCG (which is not into
gromacs at least in a standard, straight forward out of the box way)? That's
nice, would be really interesting to implement, would take long time and is
still a relativelly open-field with lot to be still explored.
I think we
Good afternoon,
The reason of this email is to ask:
is it possible to combine Martini's force field with the opls force field?
The system is conformed by dopc membrane [Modeled by Martini's force field]
with a small molecule of about 50 atoms [Modeled with opls. With all its
hydrogens].
if
On Feb 2, 2009, at 10:19 PM, DAVID RINCON wrote:
Good afternoon,
The reason of this email is to ask:
is it possible to combine Martini's force field with the opls force
field?
The system is conformed by dopc membrane [Modeled by Martini's force
field] with a small molecule of about 50
Good afternoon,
I would like to know how I can donwload the Martini force field. I have already
tried on its webpage:
http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html
But, it seems it is not working.
Thanks a lot for your kindly help.
David Rincon.
DAVID RINCON wrote:
Good afternoon,
I would like to know how I can donwload the Martini force field. I have
already tried on its webpage:
http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html
But, it seems it is not working.
The link you've posted is working just fine at the moment.
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