Hard to really know without more information. What is the starting
structure? What were your equilibration stages?
On Wed, Sep 11, 2019, 6:48 AM Bharat Manna <bharatmanna.gmail.com> wrote:
> Dear AMBER Users,
>
> I was trying to simulate a small protein (~100 residues) containing 4
> helices. During the heating (NVT) step (0K-300K), I found that two of the
> helices lost the secondary structure and turned in to coils. At the time of
> equilibrium (NPT) simulation, another one helix faced the same. I have
> tried the standard ff14SB force field along with TIP3P/TIP4PEW water
> models. In both cases, I found the same. Any suggestion, what might have
> been gone wrong?
>
> Thanks,
> B Manna
> PhD Scholar
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 11 2019 - 04:00:02 PDT
