Fabian Casteblanco wrote:
Hello Justin,
You mean that only for vdW decoupling, you would need to use soft-core
potentials? I had soft -core potentials on for decoupling the
electrostatic interactions (see below). What would I use in its
place? Thanks again for your help!
You only need s
Fabian Casteblanco wrote:
Hello Justin,
I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling. So if I take the line formed by dGtot
hello
Now it is almost clear what happened. When couple-intramol is no (default),
all pairwise vdm and charge interaction becomes bonded interaction.
All intra-molecular non-bonded interactions for moleculetype couple-moltype
are replaced by exclusions and explicit pair interactions. In this m
Da-Wei Li wrote:
hello
1. I used almost identical comands with you.
2. If I set "couple-intramol = yes". My grompp will run very fast.
From the manu, "couple-intramol = no means " all intramol
(protein-protein interaction in my case) interaction are turned to
predefind list w
hello
1. I used almost identical comands with you.
2. If I set "couple-intramol = yes". My grompp will run very fast.
>From the manu, "couple-intramol = no means " all intramol (protein-protein
interaction in my case) interaction are turned to predefind list while
"couple-intramol
Da-Wei Li wrote:
hi, all
I get another strange error. Once I turn on free energy calculation.
mdrun will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper
Da-Wei,
How do you generate your box, solvent, ions?
I use this sequence of commands:
pdb2gmx -f protein.pdb -o protein.gro -p protein.top
editconf -bt cubic -f protein.gro -o protein.gro -c -d 1.5
genbox -cp protein.gro -cs spc216.gro -o protein_b4
hi, all
I get another strange error. Once I turn on free energy calculation. mdrun
will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13
Minimu
hello
My goal is to study the solvation free energy of a fixed protein and compare
it with implicit model. The pr1. mdp is just a test case. Grompp always need
more than 10 minutes to finish for my 76 residues protein when free_energy =
yes, no matter there is PR or not, whether I switch off only
Da-Wei,
Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?
And are you doing hydration of a protein?
Thank you,
TJ Mustard
On February 7, 2011 at 10:23 AM "Justin A. Lem
Da-Wei Li wrote:
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This
is a test case only and the protein is 1UBQ. Grompp wills top for about
10 minutes then go through.
The efficiency of this kind of process will depend on the amount of available
memory on the s
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This is a
test case only and the protein is 1UBQ. Grompp wills top for about 10
minutes then go through.
***output of grompp*
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
Generated 2278 of
Dawei,
I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?
Thank you,
TJ Mustard
On February 7, 2011 at 9:31 AM Da-Wei Li wrote:
Well. It actually isn't dea
oi.org/10.1063/1.470648), would there be any downsides to having
this method in GROMACS?
best wishes,
Floris
From: Berk Hess
To: Discussion list for GROMACS users
Sent: Friday, 7 August, 2009 16:16:19
Subject: RE: [gmx-users] Re: Free Energy Calculation
All
ven not to long ago.
Berk
Date: Fri, 7 Aug 2009 07:32:33 -0700
From: floris_buel...@yahoo.com
Subject: Re: [gmx-users] Re: Free Energy Calculation
To: gmx-users@gromacs.org
Hi David and Berk,
I guess the best proper solution would be to use a Parrinello-Rahman barostat.
But in Gromacs this is cur
his can easily be
>avoided
>by using the v-rescale thermostat.
>
>Berk
>
>
Subject: RE: [gmx-users] Re: Free Energy Calculation
>Date: Thu, 6 Aug 2009 16:01:04 -0400
>From: pn...@utnet.utoledo.edu
>To: gmx-users@gromacs.org
>
>
>
&
re
> than the issues with Berendsen temperature coupling. Berendsen tcoupl can
> have
> significant effects on your ensemble. But in Gromacs 4.0 this can easily be
> avoided
> by using the v-rescale thermostat.
>
> Berk
>
> ------
> Subject: RE: [
Peter,
On Thu, Aug 6, 2009 at 3:01 PM, Nagy, Peter I. wrote:
>
> A question to the answer below:
>
>If the Berendsen barostat does not sample correctly the distribution of
> pressures
> then what guarantees that the the volume/density is correct
> at the end of the equilibration phase when
are much less severe
than the issues with Berendsen temperature coupling. Berendsen tcoupl can have
significant effects on your ensemble. But in Gromacs 4.0 this can easily be
avoided
by using the v-rescale thermostat.
Berk
Subject: RE: [gmx-users] Re: Free Energy Calculation
Date: Thu, 6 Aug 2009
A question to the answer below:
If the Berendsen barostat does not sample correctly the distribution of
pressures
then what guarantees that the the volume/density is correct
at the end of the equilibration phase when the user is advised to switch to
NVT?
Peter Nagy
The University of Toledo
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