[gmx-users] In continuous I got another warning, could anyone help me?

Justin Lemkul jalemkul at vt.edu
Wed Mar 6 12:51:10 CET 2019

On 3/6/19 1:00 AM, Najamuddin Memon wrote:
> Thirdly, change constraints=all bonds instead of h bond in nvt and npt.mdp
> files

The type of constraints required is dependent upon the force field being 
used and should not be changed ad hoc.

> On Tue, Mar 5, 2019, 11:16 PM Najamuddin Memon <najamuddinmemon63 at gmail.com>
> wrote:
>> Do nvt and npt equillibration for 1000 ps with nxtcout, etc values 500 in
>> nvt.mdp and npt.mdp file.

Output values do not affect simulation stability.

>> Secondly, this error can be removed by changing couple intramol=yes in
>> mdout.mdp file or md.mdp file.

While it is possible to use free energy options to soften nonbonded 
interactions in difficult systems, this shouldn't often be necessary. 
Proper minimization and equilibration alleviate most problems.


>> On Tue, Mar 5, 2019, 10:31 PM banijamali_fs <banijamali_fs at ut.ac.ir>
>> wrote:
>>> 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
>>> is,
>>> 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
>>> table-extension
>>> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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