Re: [AMBER] jump in monomer position

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 6 Nov 2019 16:02:50 -0500

Hi Fabian,
does this happen during the constant pressure run? It sounds like this
might be from volume scaling due to constant pressure. It will get fixed in
the next restart. Others may know if there is a way to avoid it, but what
we usually do is hand edit the prmtop to place the dimer into a single
"molecule". I wonder if there is a way to automate this (such as in
parmed)...
carlos

On Wed, Nov 6, 2019, 3:56 AM Fabian Glaser <fabian.glaser.gmail.com> wrote:

> Dear Ambers,
>
> I am working on a hetero protein dimer, and following the first MD heating
> stage, there is a slight shift of the position of one monomer with respect
> to the other, about 0.5 Ang, in fact the center of mass shifts in a single
> frame 0.8Ang at the end of the system heating equilibration, with the
> protein restrained. The following stage is a constant pressure
> equilibration as seen bellow. I dont’ see this jump of monomer a versus b
> again during the simulation. It happens only once. I have seen this in
> another system, although the subsequent analysis etc seems just fine.
>
> I don’t understand why I see it, and if this is a visualization issue? or
> a real problem?, am I doing something wrong? Why does it happen? How I can
> check it?
>
> Thanks!
>
> 1) heating
>
> &cntrl
> imin = 0, nstlim = 1000000, dt = 0.001,
> irest = 0, ntx = 1, ig = -1,
> tempi = 100.0, temp0 = 298.0,
> ntc = 2, ntf = 2, tol = 0.00001,
> ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
> cut = 8.0, iwrap = 1,
> ntt =3, gamma_ln=1., ntb = 1, ntp = 0,
> nscm = 0,
> ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100.0 nmropt=1,
> ioutfm=1, ntxo=2,
> / &wt
> TYPE="TEMP0", istep1=0, istep2=1000000,
> value1=100., value2=298., /
> &wt TYPE="END",
> / /
>
> 2) equilibration constant pressure
>
> &cntrl
> imin = 0, nstlim = 1000000, dt = 0.001,
> irest = 1, ntx = 5, ig = -1,
> temp0 = 298.0,
> ntc = 2, ntf = 2, tol = 0.00001,
> ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
> cut = 8.0, iwrap = 1, taup = 0.1,
> ntt =3, gamma_ln=1.0, ntb = 2, ntp = 1,
> nscm = 0,
> ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100. ioutfm=1, ntxo=2,
> /
>
> Best,
>
> Fabian
>
> Fabian Glaser PhD
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web http://bku.technion.ac.il/
> Tel +972 (0) 4 8293701
>
> _______________________________________________
> 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 Nov 06 2019 - 13:30:02 PST
Custom Search