Dear Mark,
I put #include "disre.itp" at the end of making a hybrid [molecule] section
as you've suggested, I got the same error after grompp.
“Fatal error: [ file "../disre.itp", line 2 ]:
Atom index (195) in distance_restraints out of bounds (1-1)”
; File 'top.top'
Justin A. Lemkul wrote:
Hi All,
I'm building a system consisting of a protein complex with a few ligands
free in solution at the outset of the simulation. I'm using genbox -ci
-nmol to insert the ligands prior to solvation. I'm using version 4.0.3
on a dual-core Intel MacBook. The followi
Mark's suggestion of a hybrid [molecule] section is a good one. Please
note the need to then include disre=simple in your .mdp file. Mark has
previously posted an enhancement request for a grompp warning if you
forget disre=simple in the .mdp file response to some confusion that I
previousl
Pathumwadee Intharathep wrote:
Dear gmx-users,
Do you know how to make distance restraint between ligand and protein in
gromacs?
I have a chain of protein binds with 4 drugs in water-lipid box, the
topology put below..
; File 'top.top' was generated; Include forcefield parameters
;
#i
Dear gmx-users,
Do you know how to make distance restraint between ligand and protein in
gromacs?
I have a chain of protein binds with 4 drugs in water-lipid box, the topology
put below..
; File 'top.top' was generated; Include forcefield parameters
;
#include "/home/bio001/02_saow/grom
Hi All,
I'm building a system consisting of a protein complex with a few ligands free in
solution at the outset of the simulation. I'm using genbox -ci -nmol to insert
the ligands prior to solvation. I'm using version 4.0.3 on a dual-core Intel
MacBook. The following command fails:
genbo
Shuangxing Dai wrote:
Hi, all gmx users:
I am doing a simulation with NaCl (and ZnO, GaN). I start with the
.pdb file. But the Gromacs cannot recognize my new atom, such as Na, Cl.
How to add new atoms to Gromacs?
I am going to use periodical boundary conditions and LJ potential,
shel
Hi Chris,
Your suggestions were helpful. Due to the nature of this problem, there
were limitations in the application of the sequence of steps that you
recommended. Specifically, the difference in the equilibrated structure
from version 3.3.x to the calculated reference center of mass from
Hello,
Could Berk or someone else answer my question regarding the new "nstlist=-1"
option in gmx4? In my understanding, the algorithm for this option is the one
used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with
"nstlist=-1" and "nstlist=1", I found the speeds were basical
Hi Xavier,
By when do you need it? You can send me one frame ( .gro) and I can
see what I can do. But no guarantees, and no time indication :(
Cheers,
Tsjerk
On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole wrote:
>
> On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote:
>
>> Hi XAvier,
>>
>> U
On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote:
Hi XAvier,
Unfortunately, you're out of luck. The coordinates do not contain
information regarding the proper orientation with respect to the
coordinate system.
No they don't.
May be I should have mentioned that I know for each
conformati
Hi, all gmx users:
I am doing a simulation with NaCl (and ZnO, GaN). I start with the .pdb
file. But the Gromacs cannot recognize my new atom, such as Na, Cl. How to add
new atoms to Gromacs?
I am going to use periodical boundary conditions and LJ potential, shell
model , apply loading
Hi Steve,
Noting Berk's comment, I should clarify that my runs were completed using 4.0.2 and were run in parallel, so you may be seeing
something different than the discrepancy that I noted from g_dist or g_traj.
Did you try the post-mdrun processing and g_dist test that I suggested here:
htt
Hi,
This issue is resolved. Using code compiled from the CVS source:
VERSION 4.0.99_development_20090120, grompp successively ran to
completion for this system.
Thank you Berk.
-Steve
Berk Hess wrote:
Hi,
I found many bugs in the cylinder pulling code.
I fixed them all for the upcoming 4.
Hi XAvier,
Unfortunately, you're out of luck. The coordinates do not contain
information regarding the proper orientation with respect to the
coordinate system.
That's the short answer. I guess you did save all atoms, at least of
proteins and lipids, in which case you could do a search for a
rota
Morteza Khabiri wrote:
Dear Mark,
thanks for your suggestion...the position restrain is very good idea which
I did it before..but I just restrain protein and after some time ligand
start to come out..I think my problem is that I don't know how to restrain
ligand?
It will be nice of you if tell m
anirban polley wrote:
Dear Sir,
In the previous older version of gromacs(3.3.x) , there is
always an option -np by which I can say about the number of processors
that I required parallel computation. But in the gromacs4.0.3 version,
I could not find that. Can you tell me how can I run
Hi,
I thought I fixed this for 4.0.3, but apparently I only committed
the fix in the head branch and not in the release branch.
The else will indeed do the trick.
Berk
> Date: Mon, 26 Jan 2009 11:10:44 +0100
> From: sam.mo...@chem.kuleuven.be
> To: gmx-users@gromacs.org
> Subject: [gmx-users]
Dear gmx developers,
I'm trying to use the generic kernel with gromacs 4.0.3,
by setting the environment variable GMX_NB_GENERIC.
However, I get a segmentation fault.
Looking at the source code in do_nonbonded(),
I found that the function (*kernelptr)() is called regardless if
kernelptr == NU
On Mon, 2009-01-26 at 10:54 +0100, XAvier Periole wrote:
> in the gmx-4.X versions you do not need to specify the number of CPU t
> grompp but only to mdrun ...
Not mdrun, but to the MPI run program (mpirun / aprun &c).
--
--
Jussi Lehtola, FM,
Dear Sir,
In the previous older version of gromacs(3.3.x) , there is
always an option -np by which I can say about the number of processors
that I required parallel computation. But in the gromacs4.0.3 version,
I could not find that. Can you tell me how can I run in gromacs 4.0.3
version
Hi,
That is not exactly correct.
In 4.0 you only need to supply -np to mpirun for running mdrun.
Already in 3.3 there was no -np option in mdrun,
but in 3.3 and 4.0 mdrun does not complain about non-existent options.
Berk
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-
in the gmx-4.X versions you do not need to specify the number of CPU t
grompp but only to mdrun ...
On Jan 26, 2009, at 10:29 AM, anirban polley wrote:
Hi,
I have run earlier in gromacs3.3.x version in parallel processor
but now I have installed gromacs4.0.3. But when I want to run program
in
Hi,
I have run earlier in gromacs3.3.x version in parallel processor
but now I have installed gromacs4.0.3. But when I want to run program
in the gromacs4.0.3, it says that
...
Invalid command line argument:
-np
Dear Mark,
thanks for your suggestion...the position restrain is very good idea which
I did it before..but I just restrain protein and after some time ligand
start to come out..I think my problem is that I don't know how to restrain
ligand?
It will be nice of you if tell me how to restrain ligand?
Hi,
Strange, I think I have really fixed all problems now.
All test systems work fine for me.
Can you file a bugzilla entry?
Please include all the files needed to run grompp
as well as the correct pull distance and the pull distance you obtained.
Berk
> Date: Sun, 25 Jan 2009 23:45:29 -0500
>
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