[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS
Stephane.ABEL at cea.fr
Wed Mar 6 11:42:58 CET 2019
Thank you Justin,
I "grepped" the corresponding atom types. Indeed they are in the cmap files
On 3/5/19 3:33 PM, ABEL Stephane wrote:
> Dear all,
> I want to performs some MD simulations of systems with a protein model with D-AA and I would like to have the confirmation that the last release of the CHARMM parameters for GROMACS (i.e. charmm36-nov2018.ff.tgz) contains the D-CMAP terms listed in the ./stream/toppar_all36_prot_c36m_d_aminoacids.str file in the original toppar_c36_jul18 archive available in the MacKerell's website ?
Yes. You can grep for the relevant atom types and see that they're there.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
Date: Wed, 6 Mar 2019 11:00:03 +0500
From: Najamuddin Memon <najamuddinmemon63 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] In continuous I got another warning, could
anyone help me?
<CALwxfC++b7RtG4+-Ua_ZM1OR7MMdp0FW8gT17Z8Na3e7+N7P6g at mail.gmail.com>
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Thirdly, change constraints=all bonds instead of h bond in nvt and npt.mdp
On Tue, Mar 5, 2019, 11:16 PM Najamuddin Memon <najamuddinmemon63 at gmail.com>
> Do nvt and npt equillibration for 1000 ps with nxtcout, etc values 500 in
> nvt.mdp and npt.mdp file.
> Secondly, this error can be removed by changing couple intramol=yes in
> mdout.mdp file or md.mdp file.
> On Tue, Mar 5, 2019, 10:31 PM banijamali_fs <banijamali_fs at ut.ac.ir>
>> Hi there,
>> Thanks for your response, but when I went to that link, it was said to
>> put -nt 1 in command line, so when I put this I get another warning that
>> Listed nonbonded interaction between particles 1 and 29
>> at distance 2.404 which is larger than the table limit 2.200 nm.
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the
>> distance in the mdp file if you are really sure that is the reason.
>> So what should I do with this?
>> Do anyone knows what should I exactly do?
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