Dear Carlos,
Yes!, this happens just at the beginning of the first constant pressure equilibration.
Forgive me my ignorance, I understand there is a volume scaling, but I don’t understand why one monomer shifts with respect to each other as a result of the scaling, and specially if that shift affects the md trajectory, or why it is fixed automatically the next restart… I would appreciate if you could elaborate a little bit.
Thanks a lot!
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
> On 6 Nov 2019, at 23:02, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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
>>
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Received on Wed Nov 06 2019 - 23:30:02 PST
