HI
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Is this warning serious?
Could any one tell me how to fix the warning?
I see nothing wrong with my .top and my .gro file.
Thank you
Lin
Chih-Ying Lin wrote:
HI
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Is this warning serious?
Could any one tell me how to fix the warning?
use a tpr file.
I see nothing wrong with my .top and my .gro file.
Sumanth Jamadagni wrote:
Hi,
I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?
Have you tried?
If yes, what
Hello, everyone,
I meet a problem when I perform the gromacs.
I fixed two C60 molecule at a certain distance(2.02 nm) by SHAKE algorithm. The
atoms have no charge on them. So the interaction between the molecules should be
the van der Waals interactions. I set the van der Waals cut off to be
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Is this warning serious?
Could any one tell me how to fix the warning?
I see nothing wrong with my .top and my .gro file.
You should have right masses in your
after edit tfe.itp , I did the command grompp and I got this error :
error input solvated.gro. Do I have to make spc.gro with tis
forcefield(gromos965a)?
No solvated.gro? Access rights? dos format?
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,
Hi Lin,
If you include bromide, you won't have excess charge... So, no need
for adding more counterions.
Cheers,
Tsjerk
On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin [EMAIL PROTECTED] wrote:
Hi
It is the water-molecule system.
For a molecule, like R-N(CH3)3-Br, I could make a pdb file
Vitaly,
This is not a grompp warning, but a warning from one of the analysis
tools. grompp will never take masses 'out of the blue', but will
always use the force field description (atom type definitions) or the
mass specified in the .top/.itp file. It will bail out if no mass is
properly defined
Tsjerk, probably you are right about grompp. I thought the user had
received this warning when preparing a system. Like genbox and so
on... So, I mean maybe he had not .tpr at that moment...
Vitaly
2008/8/21 Tsjerk Wassenaar [EMAIL PROTECTED]:
Vitaly,
This is not a grompp warning, but a
I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?
Time does not run back. :) It's a bad idea.
--
Vitaly V. Chaban
Vitaly Chaban wrote:
I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?
Time does not run back. :) It's a bad idea.
I
Dear justin
for have tfe30% after I got tfedrg.top with pdb2gmx and force field
gromos965a.
I do t this command :
editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro
genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p
topol.top -o solvated.gro
I did that command with spc.gro(I
shahrbanoo karbalaee wrote:
Dear justin
for have tfe30% after I got tfedrg.top with pdb2gmx and force field
gromos965a.
I do t this command :
editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro
genbox -cp box.gro -cs spc216.gro ci tfedrg.gro - nmol 40 -p
topol.top -o solvated.gro
I
Hi There,
I am running gromacs on parellel system using the submit command. Commands
are running fine, but the .trr file I got is not matching with the trr file
I got while running command in serial.
Also, I am getting a number of log files(equal to number of nodes I am
choosing).
How should I
Actually I think I am using the gromos force field. I have been using
Christopher Stiles page as a guide to get started with using CNT
http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were
made to ffgmx files. So I believe I am using the gromos forcefield. Is the
Â
dear sir,
           i am vidhya sankar speaking . i am not able to down
load QM/MM exampiles files since it take much time and huge memory (156Mb)
often net is disconnected
could you please send some example input files of CPMD part mainly
'CPMD_inp.tmpl'Â 'runcpmd'Â ?
Vitaly Chaban wrote:
I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?
You could also invert the initial
Hi,
Can anybody tell which visualization tool is better out of
vmd/pymol/gopenmol to visualize gromacs result.?
Thanks in advance,
Vivek
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search
vivek sharma wrote:
Hi There,
I am running gromacs on parellel system using the submit command.
Commands are running fine, but the .trr file I got is not matching with
the trr file I got while running command in serial.
Based on what analysis? Have you done gmxcheck -f1 -f2 on these .trr
In conf.gro? It will change only the first steps but will not change
the direction of the system evolution.
As I understand, the topicstarter wanted to perform the simulation
backwards...
Vitaly
2008/8/21 Jochen Hub [EMAIL PROTECTED]:
Vitaly Chaban wrote:
I wanted to perform some
Vitaly Chaban wrote:
I wanted to perform some simulations backward and forward in time (for
transition path sampling ). If I specify a negative value for 'dt' in the
mdp file, would that work for backward integration of the equations of
motion ?
Time does not run back. :) It's a bad
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: RE: [gmx-users] Re: Simulations backward in time
Date: Thu, 21 Aug 2008 16:11:56 +0200
Surely inverting the velocities changes the direction of the system evolution.
The state of the system is given by x and v. The evolution is
Yes. Namely at the very step the velocities should be inverted to
invert a time flow.
My remark was addressed namely to the word initial.
2008/8/21 Berk Hess [EMAIL PROTECTED]:
Surely inverting the velocities changes the direction of the system
evolution.
The state of the system is given by
Using a negative 'dt' in the mdp file does not not seem to cause any
simulation problems (tested on a waterbox- doesn't crash). I am not sure
if the system is evolving backwards in time though. I am not sure how to
check that.
But I think, all I require is that the equations of motion be
Hi all,
I tried to send this to the gmx-developers list several hours ago, but it never
showed up, so I'll try here. There also appears to be problems with the Admin
pages for the mailing lists (I went to check and make sure my subscription to
that list was active).
I am simulating a
On Thu, 2008-08-21 at 10:32 -0400, Sumanth Jamadagni wrote:
Using a negative 'dt' in the mdp file does not not seem to cause any
simulation problems (tested on a waterbox- doesn't crash). I am not sure
if the system is evolving backwards in time though. I am not sure how to
check that.
So
It seems because your box should be a bit longer to succeed. Try to
enlarge the side (13.2 nm) length.
2008/8/21 Andy Shelley [EMAIL PROTECTED]:
No problem the term flattens is porbably not the best technical
description. A better one would be the cnt collapses.
Andy
On Thu, Aug 21, 2008
Dear justin
I guess I did right.I add in my topoly file tfe in part of dehedrals
gd_24.(from your edit in dmso topolgy last another mail)and I
could minimize. what do you think this adding ?.any way thank you for
every thing.now about my peptide I have this error .(in c terminal
peptide is
Hi
The salt R-N(CH3)3-Br.
Could anyone tell me how to assign the force field parameter for the
salt molecule ; especially for the ion bond/ ion angle/
Does there exist dihedral angle between the ion Br and R ?
And, any differences for assigning the Van-der waal and LJ parameters
between salt
Hi Lin,
Please read the manual. By checking the Index section you'll find charge
group.
For example, there is a paragraph in page 20.
Lanyuan Lu
Date: Thu, 21 Aug 2008 09:52:35 -0700
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject:
[EMAIL PROTECTED] wrote:
David van der Spoel, can you please comment on this post of your from 2002:
long timesteps combined with dummies give me unfolding proteins while
without
dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to
shahrbanoo karbalaee wrote:
Dear justin
I guess I did right.I add in my topoly file tfe in part of dehedrals
gd_24.(from your edit in dmso topolgy last another mail)and I
could minimize. what do you think this adding ?.any way thank you for
every thing.now about my peptide I have this
Chih-Ying Lin wrote:
Hi
The salt R-N(CH3)3-Br.
Could anyone tell me how to assign the force field parameter for the
salt molecule ; especially for the ion bond/ ion angle/
There will be no such thing, unless the force field has already assigned it.
But since a covalent bond is probably
The salt R-N(CH3)3-Br.
And, any differences for assigning the Van-der waal and LJ parameters
between salt and organic molecules?
no difference.
-
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
Hi
As you described...
This is not a grompp warning, but a warning from one of the analysis
tools. grompp will never take masses 'out of the blue', but will
always use the force field description (atom type definitions) or the
mass specified in the .top/.itp file. It will bail out if no mass
Justin A. Lemkul wrote:
Nicolas Sapay wrote:
Nicolas Sapay wrote:
Hello,
I've run the gmxtest on Gromacs-3.3.2. One simple test failed:
Testing rb1 . . . *** glibc detected *** realloc(): invalid next
size: 0x082c0180 ***
sh: line 1: 27398 Aborted mdrun mdrun.out
How do I display the actual simulation box in VMD for a gromacs
configuration/trajectory? Is it possible? By default it shows only the axes.
Regards,
Suman Chakrabarty.
___
gmx-users mailing listgmx-users@gromacs.org
Hi,
to create some toy data I want to do a vacuum simulation of alanine dipeptide
with Gromacs.
I used charmm (generate command) to build the structure of alanine dipeptide.
The structure in charmm notation is ACE-ALA-CT3 and in gromacs notation
is ACE-ALA-NAC .
The charmm output is a pdb (in
1. If I have the correct information in my .top file and .gro file,
I could successfully run GROMPP command without the warning.
And, I could ignore the warning from the analysis tools.
right?
If you have got .tpr submit it to the analysis tools.
--
Vitaly V. Chaban
School of Chemistry
You should have a look in the archives of the VMD mailing-list... Or
check this page:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcbox/
Nicolas
Suman Chakrabarty wrote:
How do I display the actual simulation box in VMD for a gromacs
configuration/trajectory? Is it possible?
Hi,
I want to clarify a few of the things about the usage of g_rotacf (for
rotational correlation function for molecules). In the manual it is given
like the following:
g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
-beginfit 2.5 -endfit 20.0
I understood that -f, -s
What do I have to adjust to get rid of the error message?
did you try searching the archives?
http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html
http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html
Chris.
-- original message --
Hi,
to create some toy data
Hello. Ie been trying to run a DNA simulation with gromacs using amber99
force field. I've started with my DNA sequence complexed with the protein,
but then decided to separate them to know exactly what the problem was. Now
I am not even using the DNA sequence from my pdb file. I`ve used the NAB
All users:
I want to calculate the AFM force in afm pulling, is there a script to
obtain forces from afm pulling! In fact, g_wham can not run, it is very
depressed. Please help me!
Thank you in advance!
-
Hi Chris,
did you try searching the archives?
Yes I tried to search in archive for No default Ryckaert-Bell. types,
but I didn't find anything useful.
But I didn't had the idea to search for the string combination:
ACE+NAC+oplsaa .
With the correction of topology file it worked.
Thanks for
Hi,
to create some toy data I want to do a vacuum simulation of Alanine Dipeptide
with Gromacs.
For the production run script I used the gmx-user mailing list thread [1a-d],
the tutorial [2] and the corresponding sample script [3].
1a:
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