Hi,
I want to run mdrun -nt 12 on our cluster.
When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p
../initial/insulin.top -n ../initial/index.ndx
I got the message,
Estimate for the relative computational load of the PME mesh part: 1.00
NOTE 1 [file test.mdp]:
Hsin-Lin Chiang wrote:
**Hi,
I want to run mdrun -nt 12 on our cluster.
When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p
../initial/insulin.top -n ../initial/index.ndx
I got the message,
Estimate for the relative computational load of the PME mesh part:
Sorry for the confusing symbol.
I tried to change it in this new mail.
Hi,
I want to run mdrun -nt 12 on our cluster.
When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p
../initial/insulin.top -n ../initial/index.ndx
I got the message,
Estimate for the
If the simulation is even stable, it will be horribly inaccurate. 12 nm
cutoffs
are unheard of and 2-nm grid spacing is about 20 times too large.
Without seeing the original .mdp file that gave the high PME load, and without
a
further description about how large the system is (number of
Dear gmx-users
Good day to you
I have a system including carbon nanotube (1260atoms) and 18 Cisplatin
molecules (198atoms) =1458atoms. I have created the topology file of the
system and now I would like to run minimization on this system.
The content of my mdp file is as below;
define
Hsin-Lin Chiang wrote:
If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs
are unheard of and 2-nm grid spacing is about 20 times too large.
Without seeing the original .mdp file that gave the high PME load, and without a
further description about how large the
meisam valizadeh kiamahalleh wrote:
Dear gmx-users
Good day to you
I have a system including carbon nanotube (1260atoms) and 18 Cisplatin
molecules (198atoms) =1458atoms. I have created the topology file of the
system and now I would like to run minimization on this system.
The content of
Hi,
I am trying to calculate the density profile of head group of bilayer normal
to z direction using gromacs 4.0.7. I was trying to center the density profile
about dx/2.dy/2,0 . But, I am finding problem with using center option. I find
using -center option does not shift the bilayer to
Sanku M wrote:
Hi,
I am trying to calculate the density profile of head group of bilayer
normal to z direction using gromacs 4.0.7. I was trying to center the
density profile about dx/2.dy/2,0 . But, I am finding problem with using
center option. I find using -center option does not
g_density is not compatible with constant pressure simulations. You
must modify it to construct the bins outward from the bilayer center
when doing NPT:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055651.html
Further, trjconv -center is misleading. I actually lost a lot of
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, August 22, 2011.
For all questions about CloudBroker and the CloudBroker
That's 9 times in the last 20 days that a single user has hit the list
with an auto-reply that seems a lot like an advertisement. Can
somebody please ban this user?
The most recent example:
http://lists.gromacs.org/pipermail/gmx-users/2011-August/063991.html
--
gmx-users mailing list
On 20/08/2011 8:02 AM, Elisabeth wrote:
Dear experts,
I am intending to calculate the equilibrium density of a pure
hydrocarbon at different pressures , at 425 K. The normal boiling
point of the liquid is around 350 K. For pressures below 100 bar
densities I am getting from NPT is in
On 20 August 2011 21:20, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/08/2011 8:02 AM, Elisabeth wrote:
Dear experts,
I am intending to calculate the equilibrium density of a pure hydrocarbon
at different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K.
Hi, Justin
Sorry for the unclear message.
My box vector in .gro file are 44.22834#160; 44.22834#160; 44.22834 and the
number of atoms is 20171
The output of grompp is shown below,
I don't know if it is enough and I'm sorry I don't know how should I do after
you reply.
Could you please give me
Hsin-Lin Chiang wrote:
Hi, Justin
Sorry for the unclear message.
My box vector in .gro file are 44.22834 44.22834 44.22834 and the
number of atoms is 20171
You've set an unreasonably large box, as I expected. The box should be set in
nm, not Angstrom. 20171 atoms is a fairly small
On 21/08/2011 2:08 PM, Elisabeth wrote:
On 20 August 2011 21:20, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 20/08/2011 8:02 AM, Elisabeth wrote:
Dear experts,
I am intending to calculate the equilibrium density of a pure
hydrocarbon at
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