Hello Justin,
In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints on rest of B2AR
#ifdef STRONG_
On 28/04/10 15:13, shahid nayeem wrote:
Hi Mark
How one should be certain that this much trajectory is long enough to
get coverged ensemble.
When the observables of interest aren't changing... This is a "how long
is a piece of string?"-type question. Read some literature about
simulations of
Hi Mark
How one should be certain that this much trajectory is long enough to get
coverged ensemble.
Shahid
On 4/27/10, Mark Abraham wrote:
>
> On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Dear Mark
>>> Following your advice I started using three peptid
Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
shahid
On 4/27/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wrote:
>
>> My peptide is 26 residue alpha helix obtained from crystal structure .pdb
>> file. I am posting energy minimization, position restari
Ming Han wrote:
1__2 6__
// 3\/ \\
|||4|
\\___ /\___//
5 7
I want to know if 1-2-3-6 torsion should be included?
And if both 2-3-4-7 and 6-3-4-5 should be included?
Thanks.
I would think that proper dihedrals would not even be used for such a molecule.
The fuse
1__2 6__
// 3\/ \\
|||4|
\\___ /\___//
5 7
I want to know if 1-2-3-6 torsion should be included?
And if both 2-3-4-7 and 6-3-4-5 should be included?
Thanks.
Ming
On Tue, Apr 27, 2010 at 6:43 PM, Justin A. Lemkul wrote:
>
>
> Ming Han wrote:
>>
>> Dear all,
>>
>> I wa
Ming Han wrote:
Dear all,
I want to test a MD simulation job for the naphthalene molecule by the
oplsaa force field by. The x2top generated less number of dihedral
angles than what I expected. Do you know how many dihedral angles
should be included for the naphthalene molecule if I use oplsaa?
Dear all,
I want to test a MD simulation job for the naphthalene molecule by the
oplsaa force field by. The x2top generated less number of dihedral
angles than what I expected. Do you know how many dihedral angles
should be included for the naphthalene molecule if I use oplsaa?
Thanks a lot.
Min
Hello,
I am trying to plot radial distribution function between a atom and a
center of two atoms.
How can I calculate the centre of two atoms and further how can I use this
center to plot radial distribution funciton?
THanks
Nilesh
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Thanks J.
My mistake.
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Maurício Menegatti Rigo wrote:
Hi,
I'm trying to compute H bonds in a protein-ligand system. I got the
following error:
Program g_hbond, VERSION 4.0.7
Source code file: gmx_hbond.c, line: 565
Fatal error:
Error in func_type Position Rest
Hi,
I'm trying to compute H bonds in a protein-ligand system. I got the
following error:
Program g_hbond, VERSION 4.0.7
Source code file: gmx_hbond.c, line: 565
Fatal error:
Error in func_type Position Rest.
---
Arthur Roberts wrote:
Hi, all,
I noticed that there was an implicit_solvent term in the mdout.mdp.
However, it didn't seem operative. I am just curious. Is it going to
be implemented soon?
Implicit solvent is implemented in the development code and (as far as I have
heard) will be part
Hi, all,
I noticed that there was an implicit_solvent term in the mdout.mdp.
However, it didn't seem operative. I am just curious. Is it going to
be implemented soon?
Sincerely,
Art
Art Roberts
3950 Mahaila Ave G18
San Diego, CA 92122
cell: 206-850-7468
email: aroberts99...@yahoo.com
sk
Dear Gromacs users,
I have a box 10 X 10 X 10 with 20 solute molecules in side it. I want
to add a solvent of 25% X and 75% Y and so on to see the aggregation
behavior of my molecules in different ratio of solvents X and Y. Can
any body help me how to do this. The two solvent is mixed.
e.
tekle...@ualberta.ca wrote:
Dear Gromacs users,
I have a box 10 X 10 X 10 with 20 solute molecules in side it. I want to
add a solvent of 25% X and 75% Y and so on to see the aggregation
behavior of my molecules in different ratio of solvents X and Y. Can any
body help me how to do this. Th
Hi, all,
I am trying to do distance restraints under two different conditions
of the protein. I have both of these proteins in the same box.
Because the experimentally determined distance restraints are from the
same signal, there are distance restraints between similar atoms in
both st
Lucio Ricardo Montero Valenzuela wrote:
hello. I got the same error, because I was using an NPT ensemble to do a
position-restrained simulation, and the error disappeared when I did the
position-restrained simulation with NVT.
I would be careful about ad hoc changes to the statistical mechani
hello. I got the same error, because I was using an NPT ensemble to do a
position-restrained simulation, and the error disappeared when I did the
position-restrained simulation with NVT.
Best regards.
Lucio.
El mar, 27-04-2010 a las 16:52 +0530, vani ms escribió:
> hello
> i got the warning as the
you should remove the water and lipid bilayer COM separately.
I am not sure what you should do with your small molecule though.
Probably best to add it to the bilayer as you constrain their relative
position!
On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote:
Hi again,
Thanks Xavier for your r
ERIKSSON, EMMA wrote:
Hi again,
Thanks Xavier for your reply. I didn't know that this mdp option
existed. However, I read the manual and also checked the mdout.mdp files
for my previous simulations, and I understood it as if those are the
default settings even if you don't specify any of the
Hi again,
Thanks Xavier for your reply. I didn't know that this mdp option existed.
However, I read the manual and also checked the mdout.mdp files for my previous
simulations, and I understood it as if those are the default settings even if
you don't specify any of them in the md.mdp file. The
On 25/04/2010 10:18 PM, afsaneh maleki wrote:
Hi,
I want to calculate relative free energy associated to mutation of P1
(native protein) to p2 (mutated protein).In this mutation, Isolusine (in
P1) is mutated to Proline(in P2). With using Thermodynamic cycle:
Bilayer+P1= = => Bilayer-P1 delta G1
On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
shahid nayeem wrote:
Dear Mark
Following your advice I started using three peptide in one simulation
box. Iwas able to add these with genconf as previously in ordered
manner, generated .gro with genconf, solvated it and after energy
minimization I
shahid nayeem wrote:
My peptide is 26 residue alpha helix obtained from crystal structure
.pdb file. I am posting energy minimization, position restarint and full
MD simulation .mdp file
ref_t = 300 300
Here, you're equilibrating at 300 K...
ref_t = 500 500
and here, you're ru
My peptide is 26 residue alpha helix obtained from crystal structure .pdb
file. I am posting energy minimization, position restarint and full MD
simulation .mdp file
Energy minimization
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 3000
;
; Energy mi
Hi,
NMA is not MD - for one thing you don't run an NMA simulation for a
certain time. I suggest you read about NMA and make sure you understand
what the method does and what it can achieve before continuing. There is
some data on the manual, a lot of data on the web and even more in
books. When yo
The crash seems to be expected as by crossing the pbc the distance
will change significantly
and in way the algorithm can not handle.
Note that the overall translational motion of your system should
always be removed.
The removal of the COM motion of your bilayer should be sufficient to
vani ms wrote:
hello
i got the warning as the Warning: "1-4 interaction between 246 and 251
at distance 4.991 which is larger than the 1-4 table size 2.400 nm
These are
ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-exte
hello
i got the warning as the Warning: "1-4 interaction between 246 and 251 at
distance 4.991 which is larger than the 1-4 table size 2.400 nm
These are
ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Hi ALL,
This may sound like a very basic question, but I am still pondering over it.
I have simulated a membrane protein system for 30 ns after Steepest Descent
minimization and now I want to perform NMA. From the help pages what I
understand is that I need a very well minimized system (using l-bf
shahid nayeem wrote:
Dear Mark
Following your advice I started using three peptide in one simulation
box. Iwas able to add these with genconf as previously in ordered
manner, generated .gro with genconf, solvated it and after energy
minimization I did MD run for 10ns. Everything ran well. In
Hi all!
I have a problem regarding lipid bilayer simulations in Gromacs 4. During some
of my simulations the whole system is moving in the z direction in the box,
meaning that after some time the lipids are going out in the bottom of the box
and coming in in the top of the box, since I'm using
Dear Mark
Following your advice I started using three peptide in one simulation box.
Iwas able to add these with genconf as previously in ordered manner,
generated .gro with genconf, solvated it and after energy minimization I did
MD run for 10ns. Everything ran well. In the end when I see the traj
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