Hi all,
I found that the 99SB force field in AMBERTOOLS1.5 and GROMACS4.5.4 have
different force constants for bond and angle parameters, after converting
them to the same unit.
So for those in AMBER
[ moleculetype ]
; molname nrexcl ; TIP3P model
WAT 2
[ atoms ]
; nr typ
Sai Janani Ganesan wrote:
Hi,
Thanks for the reply!
I tried the rates, and only the terminal with positive rate gets pulled.
The first and the last amino acids are spatially oriented one behind the
other. I think defining a vector might work better, but I am not sure
why nothing happens wh
Hi,
Thanks for the reply!
I tried the rates, and only the terminal with positive rate gets pulled.
The first and the last amino acids are spatially oriented one behind the
other. I think defining a vector might work better, but I am not sure why
nothing happens when I define a pull_vec1 and pull
Concur. I just used this approach to equilibrate a box of
water/acetonitrile. If your box shrinks too much, you can probably
use editconf and genbox to replicate the equilibrated box into a
larger box of arbitrary size and shape.
MZ
On Thu, Oct 6, 2011 at 4:36 PM, Dallas Warren wrote:
> Ravi,
Ravi, not entirely sure what you are actually doing / aiming to do, but another
option is to run the system NPT, which means the box size will scale to give
the correct pressure / density, then you take that and run your NVT run. But
that means you will end up with possibly a substantially smal
Hi,
If you don't get any takers, you could always just make a huge box of water
(which usually dominates explicit-solvent MD costs) and run it. That way,
you could scale up the size of the box arbitrarily to achieve good
parallelization across that many cores. I'm not sure that'd be
scientifical
Fabian Casteblanco wrote:
Hello Justin,
I have a question about your tutorial. If I want to mutate one small
group of a molecule, I would have to not provide 'couple_lambda0' and
'couple_lambda1', correct? I would essentially have to follow sec
5.7.4 in the Gromacs manual and I have to actua
Dear Tom,
Thank you very much for your answer. I am aware of the paper you suggested
but it is not clear for all mdp parameters. My intent is the simulation of a
small organic molecule into the DPPC membrane making use of the CHARMM36 force
field. There are significant differences when I c
Hi Zhenlong,
I guess that some molecules got split over the boundaries during
equilibration. You have to make them whole before changing the box.
Better to start off with a rhombic dodecahedron though.
Cheers,
Tsjerk
On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li wrote:
> Dear all,
> My system is
Hello Justin,
I have a question about your tutorial. If I want to mutate one small
group of a molecule, I would have to not provide 'couple_lambda0' and
'couple_lambda1', correct? I would essentially have to follow sec
5.7.4 in the Gromacs manual and I have to actually provide all state A
variab
Dear all,
My system is based on Martini, needs a dodehedron box.
Initially, it was minimized and equilibrated with a cubic box smoothly. Then
I used the follow command to
translate the box in to dodehedron:
editconf -f f0.gro -bt dodecahedron -d 2 -o vesdode.gro
But with this change,
Hi Giovanni,
Yes it can, but the behaviour of the membrane can be quite dependent on
the simulation parameters used.
Check out this the mailing list archives for more details about this. I
would advise using the simulation parameters as used in the CHARMM36
paper of Klauda et al. and you sho
Dear GROMACS users,
I am interested in simulating a DPPC membrane with CHARMM 36 force
field in GROMACS. The charmm36.ff_4.5.4.tgz was downloaded by the
following web page:
http://www.gromacs.org/Downloads/User_contributions/Force_fields. When the
membrane is simulated in NPz(A=0.64nm^2)
http://30dayprofitpathways.com/bbc.php?html138
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Dear Gromacs users,
For one of our customers I have to test a cluster using a parallel
application that runs for 1 week on 113 nodes with 12 cores each. The nodes
have 20GB memory available. A large Gromacs simulation would be ideal.
Unfortunately, I do not have a proper large input file for Groma
Sai Janani Ganesan wrote:
Hi,
I am trying to pull the first from the last amino acid of a protein to
completely unfold the protein in the X direction. I chose the middle
amino acid as the reference, and the groups get pulled in the same
direction or opposite direction (which is what I want)
Hi,
I am trying to pull the first from the last amino acid of a protein to
completely unfold the protein in the X direction. I chose the middle amino
acid as the reference, and the groups get pulled in the same direction or
opposite direction (which is what I want) depending on the trial. I am
try
On 6/10/2011 11:54 PM, prakash verma wrote:
Dear All,
while energy minimization with the protein fixed i am getting
following error:
*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
*
Rigid water models and EM are not a great combination. define =
-DFLEXIBLE in the
prakash verma wrote:
Dear All,
while energy minimization with the protein fixed i am getting following
error:
*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
Check for bad contacts and/or reduce the timestep.*
Even if i am reducing timesteps its not working.
The mi
Dear All,
while energy minimization with the protein fixed i am getting following
error:
*t = 0.011 ps: Water molecule starting at atom 21089 can not be settled.
Check for bad contacts and/or reduce the timestep.*
Even if i am reducing timesteps its not working.
The minim.mdp file which i have u
francesco oteri wrote:
The author of such work published partial charges, but nothing about
other parameters.
In order to carry out any simulation, you need more than charges. If they did
any subsequent validation of the charges, they must have assigned these
parameters. If they calculat
The author of such work published partial charges, but nothing about other
parameters.
The force-fields used are gromos43A1 and CHARMM22. The GROMACS standard
distribution contains nothing about iron sulphur cluster.
Thank you
2011/10/6 Mark Abraham
> On 6/10/2011 11:24 PM, francesco oteri wr
On 6/10/2011 11:24 PM, francesco oteri wrote:
Dear gromacs users,
I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron sulphur
cluster.
Lot of approaches are present in literature. There are a lot of
papaers suggesting partial charges
but very few suggestions regarding bonded and not b
Dear gromacs users,
I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron sulphur cluster.
Lot of approaches are present in literature. There are a lot of papaers
suggesting partial charges
but very few suggestions regarding bonded and not bonded parameters.
So i am wondering if any member
Saumya wrote:
Hello all,
I am trying to simulate the DMPC Lipid Bilayer with water molecules. I
am using Charmm27 forcefield for that. I obtain the starting structure
from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue
name for the lipid molecules. I checked the "lipid.rtp
Hello all,
I am trying to simulate the DMPC Lipid Bilayer with water molecules. I am
using Charmm27 forcefield for that. I obtain the starting structure from
Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue name for
the lipid molecules. I checked the "lipid.rtp" file in Charmm27 an
Indeed, if you do the other way:
0.65084/4.184 = 0.1 ~ 0.156
Alan
On 6 October 2011 08:17, Yun Shi wrote:
> Hi Alan,
>
> So is acpype using a conversion factor of 4.184 for dihedral force
> constant?
>
> I found some dihedral constants as 0.156 in the amber format, which should
> be 0.156
Ravi Kumar Venkatraman wrote:
*Dear All,
But I scaled the solvent box according to the density
using editconf_d command line. Then I carried out EM and NVT equilibration.*
Scaling the box with editconf simply scales the coordinates of the molecules in
it, which may or may no
*Dear All,
But I scaled the solvent box according to the density using
editconf_d command line. Then I carried out EM and NVT equilibration.*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.
+91-9686933963.*
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On 6/10/2011 3:52 PM, shahid nayeem wrote:
Dear All
I want to refine a protein homology model, I did minimization but then
procheck does not give better Ramachandran plot.
EM can only do a local minimization, and there is no good reason why
that should show a marked improvement on an arbitrar
Hi Alan,
So is acpype using a conversion factor of 4.184 for dihedral force constant?
I found some dihedral constants as 0.156 in the amber format, which should
be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force
constant of 0.65084 after conversion, which is slightly off. I won
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