How to choose the positions of the dummy atoms while constraining the
angle for a linear triatomic molecule?
The topology for a such molecule ( af for example CO2 ) is as follows
[ moleculetype ]
; Namenrexcl
CO2 2
[ atoms ]
; nr type resnr residue atom cgnr charg
On 7/24/12 10:39 AM, neme...@pharm.u-szeged.hu wrote:
Thank you for the fast answer, i will do that then. Do i have to close
this thread, or it will fade by itself?
Nothing fades, everything stays archived :) But if the issue is closed, simply
stop replying to the thread, and ask any new q
Thank you for the fast answer, i will do that then. Do i have to close
this thread, or it will fade by itself?
Lukacs
>
>
> On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote:
>> I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands
>> with peptide oligomers. I have succesfully
On 7/24/12 10:14 AM, neme...@pharm.u-szeged.hu wrote:
I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands
with peptide oligomers. I have succesfully generated the .itp file needed,
and have run some simulation. The same applies to the peptide. However i
run into problems comb
I have to simulate a G0 PAMAM dendrimer, functionalized on the 4 hands
with peptide oligomers. I have succesfully generated the .itp file needed,
and have run some simulation. The same applies to the peptide. However i
run into problems combining them. It appears the specbond.dat file is only
appli
Please keep the discussion on the gmx-users list.
On 7/24/12 8:31 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response, is there only RDF calculations to reach
cutoff value?
RDF is one possible method to find out how closely atoms or molecules are
interacting, b
Dear gmx-users
I am trying to calculate the optical rotation of a molecule in solution. There
are several examples of this in the literature where they take snapshots of
molecule at intervals throughout the trajectory, calculate optical rotation,
and average them to get a solvated optical rotat
On 7/24/12 8:18 AM, SatyaK wrote:
Thanks Justin for your reply.
Going by the Gromacs file format: "position (in nm, x y z in 3 columns,
each 8 positions with 3 decimal places)"
It is not clear to me as to how many digits before the decimal point can a
coordinate column accepts in the G
Thanks Justin for your reply.
Going by the Gromacs file format: "position (in nm, x y z in 3 columns,
each 8 positions with 3 decimal places)"
It is not clear to me as to how many digits before the decimal point can a
coordinate column accepts in the Gro file- Is it 3 or 4 digits before the
d
Dear Gromacs users,
I have a query regarding the number of bins used in wham analysis.
If I have performed by simulations over 15 umbrellas (15 different
staring structures), what should be the ideal number of bins to
perform wham analysis? Does it depend on the number of umbrellas. For
example:
As others said:
type 2 virtual site
check chapter 4.7 and 5.2.2 in the manual (version 4.5.x).
Greetings
Thomas
Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org:
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 de
On 7/24/12 2:34 AM, mohammad agha wrote:
Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
It is the cutoff value that determines if two molecules are in the same cluster.
If atoms in different molecules have a distance less than
On 7/24/12 6:13 AM, Nidhi Jatana wrote:
Dear Sir/Madam
I am running simulations on a membrane protein using Desmond and I
want to calculate area per lipid for the entire trajectory. I can
convert the trajectories to those of Gromacs using VMD. What else do I
need in order to calculate area per
On 7/24/12 2:49 AM, J Peterson wrote:
Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform deletion
Dear Sir/Madam
I am running simulations on a membrane protein using Desmond and I
want to calculate area per lipid for the entire trajectory. I can
convert the trajectories to those of Gromacs using VMD. What else do I
need in order to calculate area per lipid using Gromacs?
Thanking you
Regards
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180 degree. So what is
the best way of constraining the angle for the linear molecule ?
On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham wrote:
> On 24/07/2012 6:07 PM, Broadbent, Ric
On 24/07/2012 6:47 PM, ÏéÇ« ¿× wrote:
Dear GMX users,
As parmbsc0 force field significantly improve the representation of
alpha/gamma torsions in nucleic acid simulations,i thus want to use the
combination of parm99sb+parmbsc0 in Gromacs that was frequently employed in
recent publications.
On 24/07/2012 6:42 PM, Wu Chaofu wrote:
Dear gmxers,
For some purpose, I want to constrain some angles. Note that it is
"some" but not "all", and "constrain" but not "restrain". How to do
with it?
As discussed earlier today on the list, you need to use a triangle of
bond constraints to constra
Dear gmxers,
For some purpose, I want to constrain some angles. Note that it is
"some" but not "all", and "constrain" but not "restrain". How to do
with it? Thanks a lot for any reply.
Chaofu Wu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Dear GMX users,
As parmbsc0 force field significantly improve the representation of
alpha/gamma torsions in nucleic acid simulations,i thus want to use the
combination of parm99sb+parmbsc0 in Gromacs that was frequently employed in
recent publications. However, when i searched the whole forum
On 24/07/2012 6:07 PM, Broadbent, Richard wrote:
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calcu
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (
To check it, please enter commands as below:
#grompp_d
or
#mdrun
some options appear and at the end you will get an error that .top file was not
found!
For the second question, if you don't get the .tpr file it means you have not
generate a correct simulation( however I don't now what the exa
Sir,
Sorry for missing the subject in previous mail and adding new content in the
old mail.
Thanks Sir, for your suggestions. Changing the parameters in PRODRG generated
.itp file just solved the problem. The bond lengths and hybridisation remained
the same.
The problem was there. Read your re
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