On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi wrote:
> Thank you Mark.
>
> The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and
> solvate using spc216.gro.
>
Please visualize that result. Such a command would put solvent all around
your nanotube, so it could not have an infin
can I calculate box size after NVT so that I get density of 1 or
0.99
when using pressure coupling?
Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
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?
Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:
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This is a very common post on previous ma
rom: Neha Gandhi
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing lis
Hi,
The simplest explanation is that your box size is inappropriate for the
contents. If the box wants to change size but the nanotube is restrained to
fixed positions then you have an invalid model.
Mark
On Sun, 8 Oct 2017 15:39 Neha Gandhi wrote:
> This is a very common post on previous mail
This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.
I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for n
