Dear gmx-users,
I have a short question. Did GROMACS recent force field "GROMOS96 54a7
force field" parametrize for high temperature classical MD simulation such
as 353 K?
Is there any reference paper?
Sincerely,
Sunita
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chloride solutions at high
temperatures and pressures:a simulation study
http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.992019?journalCode=gmos20
Thanks.
Sunita
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Thanks for quick response..
I tried trjcat -f 1.xtc 2.xtc -o concatenate.xtc
But its not concatenating the two, rather overwriting the 2nd trajectory to
1st one. There should be 1600 frames but output contains only 800 frames.
Thanks
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Hello Venkat,
Ya, I am sure that I use 1st.cpt to run next 40 ns job
Find below the output of trjcat
Summary of files and start times used:
FileStart time Time step
-
complex_prod1_old.xtc0.000 p
Hello Venkat,
Yeah, I think by default it will give 0 ps as start time for both
trajectories and it should be set by user using -settime flag
Correct me if I am wrong.
Regards
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. Still its
giving errorsAnyone please suggest me how to proceed further.
Thanks in Advance
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SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita@gmail.com
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>1. Protein-Ligand complex Implic
ter(s) missing or negative for atom type 'hn'
I don't understand why its again complaining about HA and N2, even if it is
present in lig.itp.
Kindly guide in tackling this problem.
Thanks in advance
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SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru
-- Forwarded message --
From: sunita gupta
Date: Mon, Nov 25, 2013 at 3:23 PM
Subject: Can't do GB electrostatics; the implicit_genborn_params section of
the forcefield is missing parameters for 9 atomtypes or they might be
negative.
To: gmx-us...@gromacs.org
Hello everyon
4. Re: (no subject) (Justin Lemkul)
>5. Fwd: Can't do GB electrostatics; the implicit_genborn_params
> section of the forcefield is missing parameters for 9 atomtypes
> or they might be negative. (sunita gupta)
>
>
> -
with this method.
Best Regards
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SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita@gmail.com
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SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email
@maillist.sys.kth.se
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>1. Cannot write trajectory frame;maybe you are out of disk
> space (Andre
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