On 14/01/12 08:30, Suman Nandy wrote:
Respected Sir,
According to suggestions, in gmxusers, I have used renumtop, although it
renumbers the ligand topology, but gives a duplicate atom label.
; ERROR: duplicate atom label '4968' for atom #4968 (already used for
atom #4968)
I used the command "./
Please post all Gromacs-related questions to the gmx-users list. I am not a
private help service. I am CC'ing the message to the list and would ask that
all further discussion be posted there.
The plot you showed was simply hydrogen bonds between some molecule and FAD,
which can easily be
ge: 1
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Re: Need Help about GROMACS.
To: Discussion list for GROMACS users
Message-ID: <4bf28b9c.9040...@vt.edu>
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Archana S Achalere wrote:
Thank you Dr. Justin for th
emkul"
Subject: Re: [gmx-users] Re: Need Help about GROMACS.
To: Discussion list for GROMACS users
Message-ID: <4bf28b9c.9040...@vt.edu>
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Archana S Achalere wrote:
Thank you Dr. Justin for the reply.
Here are the details
Archana S Achalere wrote:
Thank you Dr. Justin for the reply.
Here are the details of my simulation.
I am simulating lipid bilayer (DPPC + water) where I give equal and
opposite force (along bilayer normal) on lipid and water molecules
I am using 128 DPPC and 3655 water. The .pdb file is
Thank you Dr. Justin for the reply.
Here are the details of my simulation.
I am simulating lipid bilayer (DPPC + water) where I
give equal and opposite force (along bilayer normal) on lipid and water molecules
I am using 128 DPPC and 3655 water. The .pdb file is taken from
Prof. Tieleman's p
Regardless of whether or not you've received a response, please keep all
correspondence on the gmx-users list. I am not a private tutor. To what post
are you referring? The list is fairly high-traffic, so if it's been a long time
since you posted, don't continue to wait for a response. Pos
David M.,
Thanks for the suggestions. About the Yu et al. error bars:
> For Yu et
> al., the first number is the average from the full 5 ns simulation and
> the number in () is for the last 2 ns.
If not for the CE23Me case, I would probably assume that the discrepancy due to
doing a notorio
Jonathan,
First, a question: I know that certain values of sc-alpha are preferred for
different cases, but are there any values that definitely should not be used?
In my calculations, some hydrogens (with charges but no L-J) are mutated into
united atom methyls (with charges and L-J), so the
This is a follow-up from my post in January regarding my attempts to reproduce
some free energy of solvation calculations for modified cellulose oligomers.
First, a question: I know that certain values of sc-alpha are preferred for
different cases, but are there any values that definitely shoul
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