Thanks to everyone for the insights. I'll try running things with the cutoff
and see how it goes.
-Justin
Quoting Michael Shirts <[EMAIL PROTECTED]>:
> Hi, Justin-
>
> Have you considered -not- running PME in vacuo? If you set your
> cutoffs and rlist large enough, then you can just run with
Hi, Justin-
Have you considered -not- running PME in vacuo? If you set your
cutoffs and rlist large enough, then you can just run with simple
cutoffs, and it should run -fst-. Of course, you should compare
to the energy with PME -- if they are not equivalent, then you many
need to go back an
Yes, what he said.
On Mon, May 19, 2008 at 3:00 PM, van Bemmelen
<[EMAIL PROTECTED]> wrote:
> Hi Justin,
>
> You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no)
> cutoffs.
>
> I'm not entirely sure why PME takes such a long time, but I can give a very
> wild guess. It may hav
Hi Justin,
You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no)
cutoffs.
I'm not entirely sure why PME takes such a long time, but I can give a very
wild guess. It may have something to do with the fact that, if I remember
correctly, the Fourier transform of one (or a few)
How about you try the different options, see what they do, and then decide for
yourself how best to utilise them for whatever it is that you wish to do?
- Original Message
From: ANINDITA GAYEN <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, May 19, 2008 2:28:30 PM
Subject:
Dear Colleague.
We cordially invite you to register for the:
3rd Annual CMM 'Users Meet Developers' Workshop on QM/MM Simulations
August 21st to 23rd 2008 in Philadelphia, PA
* Goals
The primary goal of this annual workshop is to encourage communication between
users and developers of
Hi all,
I'm running some free energy calculations (in vacuo and in solution) for a set
of molecules I am trying to parameterize. All the molecules are fairly small,
about 30-35 atoms in each. The solvated calculations go smoothly, and rather
quickly (~5 hr/ns on two nodes). I am running into a
Is there a way within GROMACS to use both Buckingham and Lennard-Jones
potentials in the same simulation? So for example water-water could be
modelled with LJ and water-solute with Buckingham?
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http://ww
How to be sure that the water is moving from the leaflet to the
other leaflet? Can I see it from any analysis? How can i trace a water
that is moving due to pbc and how to originate a pdb that will show the
pdb that will be visually good for analysis (I am confused about the
-pbc nojump and -pbc wh
Date: Sat, 17 May 2008 08:48:28 +0330
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] [ angle_restraints_z ]
Hi all,
There are atoms (a1 and a2) in my small molecule coordinate file that have the
same z component:
a1: atom#22 (x1,y1,60.231)
a2: atom#45 (x2,y2,60.23
Hi,
No dipole moments are transfered from CPMD to Gromacs.
Berk.
> Date: Sat, 17 May 2008 12:44:43 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] dipole momentum calculation in Gromacs/CPMD
>
>
> Dear all,
>
> Would some one please explain how the dipole
sangeeta kundu wrote:
Dear Sir,
I want to minimize an average structure obtained from a
simulation, by conjugate gradient method.. As this method is more
efficient than steepest descent I am trying with this method. The
minimization has gone smoothly with steepest descent and l
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