On 5/13/13 8:23 PM, Marcelo Vanean wrote:
Hi. I'm with doubts concerning the charge groups. I am simulating ethylene
glycol and the only way of charged groups are neutral is putting all atoms
in only one charge group. This is advisable? Is that a problem? What is the
greatest number of atoms
On 11/5/12 9:24 AM, akn wrote:
Dear gmx users,
I'm using PME for electrostatic interactions and so I don't need to arrange
charge groups.
I think the treatment of charge groups relies more on the force field rather
than the electrostatics method. With PME, it is true that you do not
You cannot overcome it, unless you rewrite the code. IIRC, the TPI(C) code
only accepts molecules for insertion in the same charge group, as it is
stated in the error.
Best,
João
On Fri, Mar 9, 2012 at 11:05 PM, Tina Wang ttw...@princeton.edu wrote:
I'm encountering a problem in implementing
The new GROMACS 4.5.4 version of the CHARMM36 force field files are now
uploaded on the GROMACS website contributions section.
Just to note that if anyone downloaded the 4.5.4 version uploaded a few
hours ago then the atomtypes.atp file was incomplete and should download
this new version.
Hi,
Yes, this was done on purpose to reflect the different use of charge
groups in CHARMM and GROMACS. Check out the mailing list archives for
more details about this.
On another note you might like to take a look at the contributed
CHARMM36 force field (available to download on the GROMACS
Thanks a lot, I will check that out.
From: Thomas Piggot t.pig...@soton.ac.uk
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, August 5, 2011 6:48 PM
Subject: Re: [gmx-users] Charge groups in Charmm for lipids
Hi,
Yes, this was done
On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote:
Hi,
Yes, this was done on purpose to reflect the different use of charge groups
in CHARMM and GROMACS. Check out the mailing list archives for more details
about this.
On another note you might like to take a look at the contributed
Sure, I will upload a GROMACS 4.5.4 version of the force field files to
the website.
Cheers
Tom
On 06/08/11 01:34, Peter C. Lai wrote:
On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote:
Hi,
Yes, this was done on purpose to reflect the different use of charge groups in
CHARMM and
Gavin Melaugh wrote:
Hi all
Do atoms belonging to the same charge group have to be indexed
consecutively in the topology file or can you have the following.
[atoms]
1 CA 1 CGECA 1 -0.1150 12.0110
2 CB 1 CGECB 1 0.
Gavin Melaugh wrote:
Hi Justin
The two files processed.top and topol.top are the exact same. What is
worrying me is that when I look at the topol.tpr from gmxdump, my charge
groups do not seem to be specified the way I stated in the topology file.
Can you provide a relevant snippet of the
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGECA 1
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
[atoms]
; atomnr type resnr residue namecgnr charge mass
1 CA 1 CGE
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have
its own charge group (3).
Gavin Melaugh wrote:
O.K cheers
I assume that this is irrelevant in vacuum with no cut-offs
Or (for reference) with PME, I would suspect, since in this case charge groups
do not have to be net neutral.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr
Also. Obviously I arranged the charge groups like this so that they
would be neutral, I just didn't realise that the atoms comprising the
charge groups had to be in sequence.
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
As you can see atomnr 7 HC should belong to the same charge group (1) as
mohsen ramezanpour wrote:
Dear All
I read charge groups section in the gromacs manual.
I have a question.please let me know it's answer.
Is it necessary that our charge groups be made of afew number of atoms?
in the other words ,if I have a charge group with 50 atom,Is my results
valid?
mohsen ramezanpour wrote:
Dear All
Suppose I determined partial charges on atoms of my molecules.
How can I make charge groups of them?
Look for similar groups in the force field you're using, and refer to the
Gromacs manual, section 4.6.2.
For example I have a drug of 50 atom(of
Will Glover wrote:
Hi,
I have constructed a gromacs MD simulation of liquid tetrahydrofuran (at RTP)
in which I'm treating each molecule as a charge group. When using a Switch for
both the Coulomb and VdW interactions I see artifacts in the radial
distribution function of the
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
Andreas Kring wrote:
Hello all.
I have read the manual and searched the archives, but I am still a
little confused so here goes:
I am going to perform an MD simulation of a molecule consisting of 38
atoms and with a total charge of -4e (water as the solvent). For this
molecule it is not
David van der Spoel wrote:
Andreas Kring wrote:
Hello all.
I have read the manual and searched the archives, but I am still a
little confused so here goes:
I am going to perform an MD simulation of a molecule consisting of 38
atoms and with a total charge of -4e (water as the solvent). For
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