[gmx-users] In continuous I got another warning, could anyone help me?
najamuddinmemon63 at gmail.com
Wed Mar 6 07:00:47 CET 2019
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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