This would be very good! I'm working on somewhat similar thing, but I plan to
use external library for computing rigid body forces from atom forces. If
gromacs will be able to compute rigid body forces itself it will be great!
Regards,
Semen
From: "gyorgy.han
Dear All,
I need to hack mdrun in rather complex way and need some help from people, who
understand Gromacs internals really well.
My problem is the following. Each N MD steps I want to pass current coordinates
and forces to custom function, which transforms them in a certain way (doesn't
matter
could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.
Cheers,
Tsjerk
On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:
> Dear All,
> Our colleges asked me to do some rather simple
Dear All,
Our colleges asked me to do some rather simple MD of the organic-silicone
compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
not so simple because of the force field. Does anybody know about parameters
for such systems, which are adapted for GROMACS? I've only
Ok, I have found the bug.
In file xdrfile_xtc.h conditional directives should be "#ifdef __cplusplus",
not "#ifdef CPLUSPLUS" !
- Original Message
From: Semen Esilevsky
To: Discussion list for GROMACS users
Sent: Sunday, May 17, 2009 8:47:44 PM
Subject: Re
- Original Message
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Sunday, May 17, 2009 4:05:16 PM
Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Semen Esilevsky wrote:
> Ok, I've submitted a bug report. Concerning
rfile library?
Semen Esilevsky wrote:
> Dear All,
> I'm trying to add the functionality of reading xtc to my own C++ code for a
> long time, so I was looking forward for libxdrfile release. Finally it is
> released and I tried it. I included xdrfile_xtc.h and immediately got
Dear All,
I'm trying to add the functionality of reading xtc to my own C++ code for a
long time, so I was looking forward for libxdrfile release. Finally it is
released and I tried it. I included xdrfile_xtc.h and immediately got the
following error:
/usr/local/gentop/include/xdrfile/xdrfile.h
- Original Message
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Monday, March 23, 2009 12:40:19 PM
Subject: Re: [gmx-users] Trying to link C++ code with libgmx. Please help!
Semen Esilevsky wrote:
> Dear gmx users,
> I'm trying to read and writ
Dear gmx users,
I'm trying to read and write xtc files from my own code written in standard
C++. I included xtcio.h and linking with libgmx.a. However when I'm trying to
compile I get hundreds of errors like:
/usr/local/gromacs/include/gromacs/types/simple.h|124|error: reference to
‘real’ is a
> Not yet, but in 4.1 it will.
The strange thing is that it "works" in the sense that implicit_solvent = GBSA
does not crash :)
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please searc
Dear All,
I've just found that the implicit solvent code seems to work in Gromacs 4.x,
the feature I was waiting for a long time to play with. However, there is
absolutely no documentation - not a single word anywhere except the traceback
of GB options in mdout.mdp (that is how I found this out)
> I tried to remove water,by first adding water to entire system and
then removed water from sides using a tcl script.But since this system
is huge,am getting error with this procedure.
What kind of error? If you are doing this in VMD you may run our of memory if
you do not delete temporary sel
ist for GROMACS users
Sent: Wednesday, December 24, 2008 6:01:38 PM
Subject: Re: [gmx-users] g_dipoles questions
Semen Esilevsky wrote:
> Dear David,
>
> Thank you for reply! However there are still some question:
>
>
>>> Dear All,
>>> I have few questions about
Dear David,
Thank you for reply! However there are still some question:
>> Dear All,
>> I have few questions about g_dipoles, which are not explained in the manual:
>> 1) What method is used to calculate the epsilon? Is there a reference which
>> can be cited? Is it suitable for water solutions
Dear All,
I have few questions about g_dipoles, which are not explained in the manual:
1) What method is used to calculate the epsilon? Is there a reference which can
be cited? Is it suitable for water solutions?
2) I can't figure out the purpose of the option -enx. When I supply edr file
with th
Dear All,
I have few questions about g_dipoles, which are not explained in the manual
(these questions are probably mostly to developers):
1) What method is used to calculate the epsilon? Is there a reference which can
be cited?
2) I can't figure out the purpose of the option -enx. When I supply
Dear Berk,
This works perfectly with new -sys option! Could you please commit this change?
I'm starting to think that ordinary users can really improve the quality of
Gromacs now ;)
Semen
From: Berk Hess <[EMAIL PROTECTED]>
To: Discussion list for GROMACS user
lt;[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users
> Sent: Wednesday, November 19, 2008 1:57:19 PM
> Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation?
>
> Semen Esilevsky wrote:
> > Dear All,
> > Where can I find documentation about the pull code
8 1:57:19 PM
Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation?
Semen Esilevsky wrote:
> Dear All,
> Where can I find documentation about the pull code in Gromacs 4.0? As far as
> I understand old style of setting up pulling simulations in separate file
> does not work any
OMACS users
Sent: Wednesday, November 19, 2008 1:57:19 PM
Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation?
Semen Esilevsky wrote:
> Dear All,
> Where can I find documentation about the pull code in Gromacs 4.0? As far as
> I understand old style of setting up pulling simulati
Dear All,
Where can I find documentation about the pull code in Gromacs 4.0? As far as I
understand old style of setting up pulling simulations in separate file does
not work any more, but I can't figure out how to transfer pulling params
correctly to mdp file.
Any help is appreciated!
P.S. Pr
Dear gmx users,
There was a lot of messages about reading xtc files from fortran programs,
however I could not find the clear answer how to link fortran-90 programs with
the xtc routines.
The example code given in the manual does not work because the library -lxtcf
is not there. I've also tryed
Hello everyone,
I'me trying to run a very long simulation with the AFM pulling, which should be
partitioned into many smaller pieces. However, this seems that the pull code
does not preserve the force even if the position of the spring is set to what
was observed at the end of the previous run.
Ok, I've got this paper and also the original (I hope
so) paper describing the method:
J Comput Chem. 2004 Mar;25(4):479-99.
Gallicchio E, Levy RM.AGBNP: an analytic implicit
solvent model suitable for molecular dynamics
simulations and high-resolution modeling.
The method is not very easy to
;
> David van der Spoel wrote:
> > Semen Esilevsky wrote:
> >> Dear colleagues,
> >> I've searched the archives to find some
> information
> >> about the Generalized born models implemented in
> 3.3,
> >> but have found only the questions and no
Dear colleagues,
I've searched the archives to find some information
about the Generalized born models implemented in 3.3,
but have found only the questions and no answers.
I'm using custom software, which uses gromacs
topologies and force fields, so I'm interested in the
parameters for GB used in
Dear colleagues,
I've searched the archives to find some information
about the Generalized born models implemented in 3.3,
but have found only the questions and no answers.
I'm using custom software, which uses gromacs
topologies and force fields, so I'm interested in the
parameters for GB used in
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
> Semen Esilevsky wrote:
> > I have another question about g_anaeig:
> > If I use -proj option in conjuction with -first
> and
> > -last the program writes projection of only one
> first
> > eigenv
> Semen Esilevsky wrote:
> > I have another question about g_anaeig:
> > If I use -proj option in conjuction with -first
> and
> > -last the program writes projection of only one
> first
> > eigenvector. As I understand it should be one
> column
> > for e
ROTECTED]> wrote:
> Semen Esilevsky wrote:
> >>You have to use also a reference file with the
> same
> >>amount of atoms in it,
> >>like your new trajectory.
> >>
> >>Use something like trjconv or as the error msg say
> >>tpbconv to write ou
Ok, I've found the problem. It was my stupid mistake -
I forget that the filtered trajectory contains only CA
:) Thank you for help!
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
> Semen Esilevsky wrote:
> >>You have to use also a reference file with the
> same
> You have to use also a reference file with the same
> amount of atoms in it,
> like your new trajectory.
>
> Use something like trjconv or as the error msg say
> tpbconv to write out a
> gro/pdb file only with CA atoms.
No, this is not an issue here. I've made the same but
without -ref option
Dear gmx users,
I've found a strange problem in g_anaeig.
I'm trying to project the trajectory into few first
eigenvectors. For this I first do:
g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit
-ref -pbc -tu ns
Chosing CA group for matrix construction.
Then I pick the resulting file eigenvec.t
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