Hi,
This issue has been resolved.
It was indeed a problem of a pull group consisting of multiple molecules.
In this case the choice of the pull_pbcatom mdp parameter was critical.
If you do not set this, it takes the numerically middle atom of the group.
In this case that was an atom in a lipid h
Yanmei Song wrote:
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
1 2 5 6 10.03.77 30.03.77 3 ; dih CAA
CBF OAW CBH
2 5 6 9 10.03.77 30.03.77 3 ; dih CBF
OAW CBH OAY
5 6 9 10 10.03.77 30.03.77
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
1 2 5 6 10.03.77 30.03.77 3 ; dih CAA
CBF OAW CBH
2 5 6 9 10.03.77 30.03.77 3 ; dih CBF
OAW CBH OAY
5 6 9 10 10.03.77 30.03.77 3 ; dih OAW
CBH
Yanmei Song wrote:
What makes me so confused is that I used this top for the MD run using
ffoplsaa.itp and the there are no error message. Also I got a good
result compared to experiment. Does it mean that what I did is totally
wrong with using this top in combination with OPLS?
Well, the nu
What makes me so confused is that I used this top for the MD run using
ffoplsaa.itp and the there are no error message. Also I got a good
result compared to experiment. Does it mean that what I did is totally
wrong with using this top in combination with OPLS?
Also if I used the atom type in opls_
Yanmei Song wrote:
Hi,Justin:
Thanks for your response.
I have read that part and still confused. Does it mean that if I
choose the ffoplsaa.itp in my top, I used the RB potential for
Dihedrals or the periodic type? Also actually I can only get the
parameters for phi, cp and mult (listed abov
Hi,Justin:
Thanks for your response.
I have read that part and still confused. Does it mean that if I
choose the ffoplsaa.itp in my top, I used the RB potential for
Dihedrals or the periodic type? Also actually I can only get the
parameters for phi, cp and mult (listed above) Can I use these
para
Yanmei Song wrote:
Hi,
I am using ffoplsaa.itp as my force field to do a simulation using GROMACS.
I have a question about how to write the parameters in dihedrals in
the itp file.
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
1 2 5 6 10.03.77 30.03.77 3 ;
Yanmei Song wrote:
Hi,
I am using ffoplsaa.itp as my force field to do a simulation using GROMACS.
I have a question about how to write the parameters in dihedrals in
the itp file.
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
1 2 5 6 10.03.77 30.03.77 3
Hi,
I am using ffoplsaa.itp as my force field to do a simulation using GROMACS.
I have a question about how to write the parameters in dihedrals in
the itp file.
[ dihedrals ]
; ai aj ak al fuc0, c1, m, ...
1 2 5 6 10.03.77 30.03.77 3 ; dih CAA
CBF OAW
Hi,
It's in the gmx4.0 manual. Just check the part for mdp options. I guess it is
the method in DLPOLY and many text books.
Lanyuan
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 23:28:25 +0100
Hi,
Any docume
Hi,
No warning was found. Is it because the use of "User" vdw potential?
The mdp file is the following:
title= A
cpp = cpp
include = -I../top
define =
integrator = md
dt = 0.001
nsteps
Liu Shiyong wrote:
Hi,
Thank for your helpful reply.
I understand your feeling. If you have time, please see the following.
mdrun has an option to output the final structure(-c). I just knew it
after reading your post and checked again :<
Thanks .
Firstly, I run a minimized com
Liu Shiyong wrote:
Hi,
*Step 2:*
Starting structure: clean2.pdb
I am trying to calculate the energy according to energy groups
pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i
clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1
make_ndx -f clean2.pdb -o clean
Hi,
Thank for your helpful reply.
I understand your feeling. If you have time, please see the following.
mdrun has an option to output the final structure(-c). I just knew it after
reading your post and checked again :<
Thanks .
Firstly, I run a minimized command to get the minimized
Hi,
Any documentation on how this is actually done?
Sounds interesting!
XAvier.
On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:
Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to
increase rvdw. So the buffer is zero and the system needs to update
the nblist every s
Hi,
But grompp should have given a warning about this.
You should have only obtained a tpr file when using the -maxwarn option of
grompp.
Or did grompp not give a warning about the buffer being too small?
Berk
From: lulany...@msn.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] "nstlist=
Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to increase
rvdw. So the buffer is zero and the system needs to update the nblist every
step, which is obviously wrong. After I corrected the mistake, the speed for
"nstlist=-1" is roughly three times faster as I expected.
> I guess that what you want to do is exactly what the decouple mdp options do.
> You probably don't need modify any topology files.
> If couple-intramol=no (default) than all intra-molecular interactions are not
> turned
> off and are plain LJ/Coulomb without cut-off.
Ah, this was implemented, t
Hi,
This looks like a bug, unless you have very exotic settings.
Could you mail me all your input files required to run grompp?
Berk
> Date: Wed, 28 Jan 2009 13:46:46 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] free_energy = yes & init_lambda = 0.0
Hi Berk,
the difference remains when utilizing double precision:
free energy code on with lambda=0.00: Coulomb (SR) = -3.23064e+05
free energy code off: Coulomb (SR) = -3.22653e+05
Here are the full double precision values:
; Free energy control stuff
free_energy = no
Energies
Liu Shiyong wrote:
Hi,
Did you get my script ?
As I said just a few days ago, I don't run jobs for people. I only have
allocated time on our University's cluster, which I need for myself.
That said, it is also very difficult to go through someone's scripting, laden
with variables that
Liu Shiyong wrote:
Fatal error:
atoms 4176 and 4182 in charge group 1767 are in different energy groups
PDB:
ATOM 4176 OG SER A 541 -13.599 44.346 39.228 1.00 0.00
S1
ATOM 4177 N ALA A 542 -12.827 48.211 42.079 1.00 0.00
A1
ATOM 4178 CA ALA A 5
Hi,
In the manual:
" Consider a water molecule interacting with another atom. When we would
apply the cutoff an on atom-atom basis we might include the atom-Oxygen
interaction(with a charge of -0.82) without
the compensating charge of the protons and so induce a large dipole moment
over t
Hi,
Did you get my script ?
I dump a frame from .trr file.
I did not define xtc-grps
On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>> Hi,
>>
>> I got an error when do grompp: The input PDB file comes from the output
>> of GROMACS by trajconv command.
>>
I see two potential problems that might arise with very large force constants.
1. If you start far from equilibrium your system will most definitely
crash. It appears that this is not going to be an issue for you here
though.
2. The less mass in your groups and the higher the force constant
Thanks Berk and Michael for all of your assistance,
Chris.
-- original message --
I guess that what you want to do is exactly what the decouple mdp options do.
You probably don't need modify any topology files.
If couple-intramol=no (default) than all intra-molecular interactions
are not turn
Hi,
I have rather elementary questions regarding force constants used in
restraining position/orientation:
- I have imposed a force with constants kx, ky, and kz =10^6
kJ/mol/nm^2 on a particular atom of a peptide to harmonically position
restrain the molecule inside a bilayer. Is it a
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Hi,
I guess that what you want to do is exactly what the decouple mdp options do.
You probably don't need modify any topology files.
If couple-intramol=no (default) than all intra-molecular interactions are not
turned
off and are plain LJ/Coulomb without cut-off.
Berk
> Date: Wed, 28 Jan 2009
Hi Jason,
Unfortunately for you this is not the gmx.com-mail-users forum, but the
gmx-shorthand-for-the-gromacs-program-users forum. So unless you want to try
and simulate wildlife - for which there are better programs - you're
probably better off at www.gmx.com. Now, if I help you out, am I ellig
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] free_energy = yes & init_lambda = 0.00 does not
yield identical energies to free_energy = no.
Date: Wed, 28 Jan 2009 10:48:57 +0100
Hi,
I would also expect the same results.
I have no clue what kind of sys
Hi,
I would also expect the same results.
I have no clue what kind of system you have.
But check that it is not an accuracy issue.
Could you recalculate the energies in double results.
Berk
> Date: Tue, 27 Jan 2009 20:00:23 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Sub
Hi,
You can mail the system to me.
Please include all the details required to run the system
and the different results you get with the exact Gromacs version numbers.
Berk
> Date: Wed, 28 Jan 2009 00:52:06 -0500
> From: fied...@umich.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Tr
Hi,
I assume you did not only change nstlist, but also other mdp settings, or not?
Changing only nstlist from 1 to -1 should result in nearly equal or much faster
speeds.
For efficient simulations with nslist=-1 you need to set an appropriate
buffer region (rlist > rcoulomb=rvdw). In 4.0 you h
Please advise how I can contact a GMX administrator if I am having trouble
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