wara boon wrote:
Hello,
I pull molecule into membrane by MD simulations but it error about
processing topology...
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp
Opening library file /home/Ell/groma
Hello,
I pull molecule into membrane by MD simulations but it error about
processing topology...
Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp
Opening library file
/home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp
Opening library file
/home/Ell/gromacMPI/share/gromacs/
jayant james wrote:
Hi!
Oh!! I see that nnodes: 1. So does that mean that the job I gave is not
running on four processors? If so how am I to solve this problem?
You haven't configured your MPI system with a suitable hostfile/whatever
for your machine, probably.
Mark
___
Hi!
Oh!! I see that nnodes: 1. So does that mean that the job I gave is not
running on four processors? If so how am I to solve this problem?
thanks
JJ
On Wed, Jun 17, 2009 at 9:10 PM, Mark Abraham wrote:
> jayant james wrote:
>
>> Hi Mark!
>> Thanks for the tip I got it the mpi mdrun running on
wara boon wrote:
Dear, gmx-users
I can't pull molecule into DPPC lipid bilayer. I want file.mdp
to use MD simulations.
Please.
That won't fix your problems. If you need to learn, do some tutorials
and read some documentation and try things out.
Mark
__
Dear, gmx-users
I can't pull molecule into DPPC lipid bilayer. I want file.mdp to use
MD simulations.
Please.
From
Wara
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Plea
jayant james wrote:
Hi Mark!
Thanks for the tip I got it the mpi mdrun running on my quad core
machine. I just have one small clarification. In the output file md.log
I see this message
"Started mdrun at node (0)"
I monitor my processor's load using gkrellm to see how many are running.
Whe
hi gmx-users
i was reading , in other post, the posibillity to run a new molecule without
create new .rtp file , but when i run that program, he gives me the
next error message
Program x2top, VERSION 3.3.3
Source code file: ../../../../src/kernel/x2top.c, line: 206
Fatal error:
Could only find a
Hi Mark!
Thanks for the tip I got it the mpi mdrun running on my quad core machine. I
just have one small clarification. In the output file md.log I see this
message
"Started mdrun at node (0)"
I monitor my processor's load using gkrellm to see how many are running.
When I started the mdrun ( mp
Yanmei Song wrote:
Dear Users:
I was running a system by non-equilibrium MD using a plain Cut-off for
the electrostatics:
title = water
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps
animesh agarwal wrote:
hello,
I want to stop my simulation in between after the density of
system reaches 300kg/m3. Is there any possible way of doing this?
Not in an automated fashion. Obviously, you will have to look (manually
with g_energy) at a post-equilibration time-averaged d
Dear Users:
I was running a system by non-equilibrium MD using a plain Cut-off for the
electrostatics:
title = water
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 50 ; tot
hello,
I want to stop my simulation in between after the density of system
reaches 300kg/m3. Is there any possible way of doing this?
Thank you.
--
==
Animesh Agarwal
M.Tech(Integrated 5 yrs.)-Part III
Industrial Chemisty
Deptt. of Applied chemistry
I.
Hello. I am trying to access the videos from EMBO course available in
Gromacs' wiki but I can't have access to any of them. Are they
available only for a strict community or something like that?
I also would like some advice on how to perform a calculation of
free-energy of dimerization between two
Anna Marabotti wrote:
Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comme
Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.
Hi Dorota, please keep all such correspondence on the gromacs mailing
list. One can then send somebody a personal email indicating that you
would appreciate it if they took a look. I have copied this answer to
the list. Please respond there.
Quoting Dorota Jamróz :
Hallo Chris,
While sea
Anna Marabotti wrote:
[ moleculetype ]
; Name nrexcl
SDS 3
; Include topology for SDS
#include "SDS.itp"
Isn't this moleculetype already specified within SDS.itp? Perhaps posting the
contents of SDS.itp will help solve this issue; the rest of the topology seems
fine, except this
Thank you guys
Indeed, it's better have all programmes in double version anyway.
But now, I may be dreaming, but how 'impossible' is to have one single
binary able to work with single or double precision with a simple
input option or env variable? At least on Mac one can have more than
one binary
Dear all,
thank you for continuous support. Here briefly what I made:
1) I deleted SDS from the first [moleculetype] section of the old .top file =
doesn't work
2) I added a new [moleculetype] section after #include "ions.itp", followed by
#include "SDS.itp" (just before
[ system ] and [ molecul
Stefano Meliga wrote:
Dear Gromacs users,
I need to produce a list of the covalent bonds of my protein structure
in the format:
Atom1 Atom2 binding energy
12 50 kcal/mol
13 150 kcal/mol
...
The binding energy is not the pote
Thomas Schlesier wrote:
Hi,
i think another problem lies here:
; Include water topology
#include "spc.itp"
.
; Include generic topology for ions
#include "ions.itp"
; Include topology for SDS
#include "SDS.itp"
[ system ]
; Name
Protein in water with SDS
[ molecules ]
; Co
Berk Hess wrote:
Hi Berk,
Thanks for your feedback.
I think there is still a general issue with optimizing the PME settings
(or settings for any electrostatics method) for MD simulations.
The question is what exactly one should optimize.
If you do a single point calculation, you might only want
Dear Gromacs users,
I need to produce a list of the covalent bonds of my protein structure
in the format:
Atom1 Atom2 binding energy
12 50 kcal/mol
13 150 kcal/mol
...
The binding energy is not the potential calculated by gro
> Date: Wed, 17 Jun 2009 15:17:53 +0200
> From: er...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] programmes to have in double precision besides
> mdrun_d
>
> Jussi Lehtola skrev:
> > On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote:
> >
> >> Hi,
> >>
> >> Nothin
Thomas Schlesier wrote:
Hi,
i think another problem lies here:
; Include water topology
#include "spc.itp"
.
; Include generic topology for ions
#include "ions.itp"
; Include topology for SDS
#include "SDS.itp"
[ system ]
; Name
Protein in water with SDS
[ molecules ]
;
Hi,
i think another problem lies here:
; Include water topology
> #include "spc.itp"
>
.
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> ; Include topology for SDS
> #include "SDS.itp"
>
> [ system ]
> ; Name
> Protein in water with SDS
>
> [ molecules ]
> ; Comp
Ok. You meant I have to cross check these parameters before getting in to
simulation.I will do that
Thank you very much for your replies.
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Justin A. Lemkul"
To: "Discussion list for GROMACS users"
Sent: Wednesday, June 17, 2009
* Berk Hess [2009-06-17 13:54:07 +0200]:
Hi,
I think there is still a general issue with optimizing the PME settings
(or settings for any electrostatics method) for MD simulations.
The question is what exactly one should optimize.
If you do a single point calculation, you might only want to m
Anna Marabotti wrote:
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but they
Jussi Lehtola skrev:
On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote:
Hi,
Nothing needs to be double precision.
Why do you want mdrun in double precision?
The only common reason for this is normal mode analysis,
in which case you need all the tools involved in double precision.
For norma
On Wed, 2009-06-17 at 13:45 +0200, Berk Hess wrote:
> Hi,
>
> Nothing needs to be double precision.
>
> Why do you want mdrun in double precision?
> The only common reason for this is normal mode analysis,
> in which case you need all the tools involved in double precision.
> For normal MD simula
Anna Marabotti wrote:
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but th
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but they are present in the orig
Marc F. Lensink wrote:
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote:
The .mdp file seems reasonable. QM charges are not necessarily the end
result in Gromos parameterization. In fact, such calculations are often
unnecessary. In my experience, assigning charges based on f
prasun kumar wrote:
Dear users
I am trying to know how gromcas is adding hydrogens so fastly and for it
I have downloaded the source code also, but not getting any thing. Can
any one please brief me so that I can initiate by myself.
The algorithms are described in the manual.
Mark
_
Dear users
I am trying to know how gromcas is adding hydrogens so fastly and for it I
have downloaded the source code also, but not getting any thing. Can any one
please brief me so that I can initiate by myself.
Thanx in advance
with regards
PRASUN (ASHOKA)
__
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote:
>
> The .mdp file seems reasonable. QM charges are not necessarily the end
> result in Gromos parameterization. In fact, such calculations are often
> unnecessary. In my experience, assigning charges based on functional groups
>
Hello Mark,
the point why I ask all this questions is that my final goal is to
enhance the SPME algorithm in Gromacs. As it is well know, that SPME is
not momentum conserving in case the forces are derived with analytical
differentiation, that means the reciprocal forces stem from the
deriv
Hi,
I think there is still a general issue with optimizing the PME settings
(or settings for any electrostatics method) for MD simulations.
The question is what exactly one should optimize.
If you do a single point calculation, you might only want to minimize
the force error. But for MD you might
Hi,
Nothing needs to be double precision.
Why do you want mdrun in double precision?
The only common reason for this is normal mode analysis,
in which case you need all the tools involved in double precision.
For normal MD simulation there is nearly never a need for
double precision.
Actually md
Remember that for PBC=xyz, the neighbor search is faster, so I suggest using
PBC with a very large box.
--Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
___
gmx-users mailing listgmx-us
Alan wrote:
Hi there,
I usually create only mdrun_d (double precision), although I am not a
hard user, however, doing some usage lately, I caught asking me if
'grompp' should be double too, and then what else.
So, is there any reason for others programme to go double besides
mdrun? If so, whi
Hi there,
I usually create only mdrun_d (double precision), although I am not a
hard user, however, doing some usage lately, I caught asking me if
'grompp' should be double too, and then what else.
So, is there any reason for others programme to go double besides
mdrun? If so, which programmes on
Ms. Aswathy S wrote:
hi Justin,
I tried the NVT once with certain changes in the parameter file. Now its
finished the 10 ps. But I have used the charge as the same from the
antechamber program. Do you think the result will be reliable? Please check
the mdp file attached for NVT.
The .mdp fi
Hi Justin,
Just to let you know that after reinstalling everything again with
Fink it worked fine. I have no idea I hade such a problem.
Alan
On Mon, Jun 15, 2009 at 23:05, Alan wrote:
> Hi Justin,
>
> Please, confirm this, you mean that this pdb worked for you with '-ignh'?
>
> Gosh...
>
> So I
Anna Marabotti wrote:
Dear gmx-users,
I would like to setup a simulation of a protein in a mixture SDS/water using GROMACS 3.3.1.
I proceeded in this way:
- after pdb2gmx, I created with editconf a cubic box of 10 nm per side centered
on my protein:
editconf -f my_prot.gro -o my_prot_box.gro
Dear gmx-users,
I would like to setup a simulation of a protein in a mixture SDS/water using
GROMACS 3.3.1.
I proceeded in this way:
- after pdb2gmx, I created with editconf a cubic box of 10 nm per side centered
on my protein:
editconf -f my_prot.gro -o my_prot_box.gro -bt cubic -box 10 -c
-
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