ers, the .gro file will
suffice, provided you use an adequate equilibration scheme.
-Justin
regards,
sharada
*/-- Original Message --/*
From: "Justin A. Lemkul"
To: "Gromacs Users' List"
Date: Sat, 31 Jan 2009 07:35:42 -0500
Subject: Re: [gmx-users] Melittin in methano
--
From: "Justin A. Lemkul"
To: "Gromacs Users' List"
Date: Sat, 31 Jan 2009 07:35:42 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> Hello Justin,
>
> Thanks for the reply . I apologise for the repeat mail. The parameters
> are for f
A. Lemkul"
To: Discussion list for GROMACS users
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> rlist = 0.5
> rcoulomb = 1.4
> rvdw = 0.8
You are using cut-off electrostatics by default, so you are probably
getting
som
to a change in the
simulation or this value holds good only if reaction field is on ?
sharada
-- Original Message --
From: "Justin A. Lemkul"
To: Discussion list for GROMACS users
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
>
Dear Justin,
Even with the new force field I am getting the same result.
The methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these
Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001
648
1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643
1MeOH O2 2 1.978 1.415 1.082 0
sharada wrote:
rlist = 0.5
rcoulomb= 1.4
rvdw= 0.8
You are using cut-off electrostatics by default, so you are probably getting
some bad artifacts (use PME instead). Also, the values of rlist, rcoulomb, and
rvdw you are using do not correspond
Dear Justin,
Even with the new force field I am getting the same result.
My methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these
Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001
648
1MeOH Me11 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643
1MeOHO2
an 2009 08:47:34 -0500
Subject: Re: [gmx-users] Melittin in Methanol...
sharada wrote:
> Hello,
>
> I am doing a simulation of melittin molecule in methanol box for 3 ns.
> I am finding that it is unfolding very rapidly and is behaving more like
> in water.
> Melittin beha
sharada wrote:
Hello,
I am doing a simulation of melittin molecule in methanol box for 3 ns.
I am finding that it is unfolding very rapidly and is behaving more like
in water.
Melittin behaviour in water, methanol and also in lipids is well
documented and known since quite some time. I am
Hello,
I am doing a simulation of melittin molecule in methanol box for 3 ns. I am
finding that it is unfolding very rapidly and is behaving more like in water.
Melittin behaviour in water, methanol and also in lipids is well documented and
known since quite some time. I am using the methanol21
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