hello:
I am quite confused on how to repeat our MD in Gromacs. If we started
from the same equilibrated .gro file with "gen_vel= no" in
md.mdp, we may get "exactly" the same results which cannot be treated as
reasonable repeated running. However, if we use "gen_vel=yes" for each
rou
On 11/20/12 5:42 PM, jhon michael espinosa duran wrote:
Hi all.
I am trying to simulate a protein initially at 0K
in water at 310K. I couple the water to 310K with
tc=0.5 and the Protein is decouple tc=-1.
The idea is analyze how is the transfer of energy from the
water to the protein.
The
Hi all.
I am trying to simulate a protein initially at 0K
in water at 310K. I couple the water to 310K with
tc=0.5 and the Protein is decouple tc=-1.
The idea is analyze how is the transfer of energy from the
water to the protein.
The interesting thing is that after 200ps the temperature of the
Virtual sites also have a hidden benefit - not only can you take a longer
time step, but the width of the distribution of PE is relatively wider, so
you can have higher exchange probability for the same temperatures.
Mark
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale <
chris.ne...@mail.utor
there is nothing wrong about the rdf, except for some noise that would
disappear
for a longer simulation. the fact that you have a region with rdf values
below 1 is
just a diagnosis for the excluded volume in your system (the protein is dry
inside,
so the volume occupied by the protein do not contr
Indeed, they must be binary identical to each other, no matter what.
I am sending two rdf plots for a lipid oxygen atom and water oxygen,
plots are identical (lipids inside a spherical micelle).
cheers
Andre
On Tue, Nov 20, 2012 at 12:01 PM, Thomas Schlesier wrote:
> The rdf should not depend on
On 11/20/12 3:55 PM, Parisa Rahmani wrote:
Yes, I ran two test simulations , one with 5 cpu and another with 1;
5 cpu simulation :
step 50380, will finish at Wed Nov 21 01:46:25 2012
step 50020, will finish at Wed Nov 21 01:48:36 2012
step 50320, will finish at Wed Nov 21 01:46:49 2012
step 50
On 11/20/12 3:38 PM, Ali Alizadeh wrote:
Dear Justin
I am using MD instead of steep, and i have a problem, I do not know
value of emtol so that energy of system reaches to -51 kj/mol, i
determine it then run it but it reaches to -30 kj/mol(only for 1ns)
original results :
http://alichemica
Yes, I ran two test simulations , one with 5 cpu and another with 1;
5 cpu simulation :
step 50380, will finish at Wed Nov 21 01:46:25 2012
step 50020, will finish at Wed Nov 21 01:48:36 2012
step 50320, will finish at Wed Nov 21 01:46:49 2012
step 50270, will finish at Wed Nov 21 01:47:07 2012
*T
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] Im Auftrag von Justin Lemkul
> Gesendet: Dienstag, 20. November 2012 18:33
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
>
>
>
> On 11/20/12 1
>I've never had an issue with similar commands. Can you provide us with your
>full g_rdf command line? Have you verified that the index group for the
>arginine residue is correct? Can you provide a link to an image of the
>resulting RDF?
>-Justin
My full g_rdf command line is as in my first
On 11/20/12 1:04 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for the quick reply
Dear All users
I want my energy minimization of my system is converged to considered
value, when i do it,
It is converged because it reachs to Fmax and i see this message :
Steepest Descents converged to Fm
On 11/20/12 12:29 PM, tarak karmakar wrote:
Thanks Justin for the quick reply.
Is there any problem with the algorithms ??
I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
has been used to constrains the H-covalent bonds.
tau_t = 1 ps
tau_P = 1 ps
I got the mean pressure a
It took me quite a while to get to grips with this and, since the question was
asked about a year ago by someone else with no response, I thought I'd share my
insight.
LJ potentials: Its important to note the slight difference from the widely
used form. You need to convert Ro to sigma by divid
Thanks Justin for the quick reply.
Is there any problem with the algorithms ??
I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
has been used to constrains the H-covalent bonds.
tau_t = 1 ps
tau_P = 1 ps
I got the mean pressure at ~130 bar.
Previously with the same initial co
On 11/20/12 12:17 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply,
1- In the first plot, unit of y axis is kj/mol, and you said above i
should use -nmol, i confused, Why is the unit of y axis kj/mol
without using -nmol?
Because that's the energy unit Gromacs alway
On 11/20/12 11:30 AM, Ali Alizadeh wrote:
Dear All users
I want my energy minimization of my system is converged to considered
value, when i do it,
It is converged because it reachs to Fmax and i see this message :
Steepest Descents converged to Fmax < 10 in 31702 steps
Potential Energy
On 11/20/12 11:26 AM, tarak karmakar wrote:
Dear All,
I want to keep the pressure at 1.0 bar during the NPT simulation. But
it is fluctuating around 130 bar. So can anyone please inform me
whether I have missed any keyword in my .mdp file OR is it because of
the tau_p which I set 1s 1.0 ps.
On 11/20/12 9:02 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to simulate protein based on my own LJ parameters between
different types of residues. I will be given sets of parametrs for
given sizes of beads to then apply them and valide by atomistic
simulations. My question:
1. What is th
On 11/20/12 9:00 AM, 闪耀星空 wrote:
Dear Justin，
Thank you for your help！I edited a parameter about HPO4 in force field 43a1 by
myself as follows：
[ PO4 ]
[ atoms ]
P P1.924 0
O1OM -1.127 0
O2OM -1.127 0
O3OM -1.127 0
O4OA -0.9
On 11/20/12 8:43 AM, Parisa Rahmani wrote:
Thanks for your reply.
I have also tried installing with _mpi suffix
Here is the output of ldd:
gromacs3.3/bin$ ldd mdrun_mpi
linux-vdso.so.1 => (0x7fff4658c000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x7f7d7afe9000)
libfftw3f.so.3
Dear Gmx Users,
I want to simulate protein based on my own LJ parameters between
different types of residues. I will be given sets of parametrs for
given sizes of beads to then apply them and valide by atomistic
simulations. My question:
1. What is the best way to build different sizes of beads fo
Dear Justin，
Thank you for your help！I edited a parameter about HPO4 in force field 43a1 by myself as follows：
[ PO4 ] [ atoms ] P P 1.924 0 O1 OM -1.127 0 O2 OM -1.127 0 O3 OM -1.127 0 O4 OA -0.949 0 H4 H 0.404 0 [ bonds ]
The rdf should not depend on the choice 'which is group A and which is
group B'! Not if the system is well equilibrated and not if you consider
only a single snapshot (in that case the rdf looks like garbage if the
system is not really huge, but the RDF(A-B) and RDF(B-A) must be the same).
I m
Thanks for your reply.
I have also tried installing with _mpi suffix
Here is the output of ldd:
gromacs3.3/bin$ ldd mdrun_mpi
linux-vdso.so.1 => (0x7fff4658c000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x7f7d7afe9000)
libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x7f7d7ac76000
On 11/20/12 4:03 AM, 闪耀星空 wrote:
Hi,
HPO4 has dihedral or not??If it has,which one?
There likely is a dihedral you need to use (since there are 4 atoms in O-P-O-H),
but the second answer depends on which force field you are using. Without
knowing that, no one can say.
-Justin
-
On 11/20/12 2:13 AM, cuong nguyen wrote:
Dear,
Thanks a lot for your suggestion Justin.
I have a box 3 3 20 and want to plot the temperature along the z axis. I
did the commands:
g_energy -f NVT_20ns.edr -s topol.top -o temp
g_analyze -f temp.xvg -dist temp.xvg
and got the results:
281.9 0
On 11/20/12 1:40 AM, Ali Alizadeh wrote:
Dear All users
I want my energy minimization of my system is converged to considered
value, when i do it,
It is converged because it reachs to Fmax and i see this message :
Steepest Descents converged to Fmax < 10 in 31702 steps
Potential Energy = -1
On 11/19/12 11:37 PM, rama david wrote:
Hi ,
I am using G 96 53a6 ff with spc water model.
system has -32 charge...( ligand + protein...ligand is small peptide)
The charge on ligand is Zero
I am using the box of 13 nm dimension.
new system size : 10.583 7.915 6.259
shift : 1.932
the opening statement "from the statistical mechanical standpoint" means a
thorough sampling has been attained, so I do agree that the reference group
choice would matter for an every day situation. Thoroughness is not
attainable
for most complex systems we might be interested in.
On Tue, Nov 20,
Hi,
HPO4 has dihedral or not?? If it has,which one?--
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