Dear David and Daniel,
thanks for your help!
Two more questions for you:
1. David, how do I distinguish weak thermostat and a strong(?) one?
I'm running my simulations with Langevin thermostat, collision frequency
(gamma_ln) of 1.0, TIP3P water model in 300K - should I be worried?
2. Daniel, I've tried the 'temperature' command in cpptraj, but I got
zeros. I'm probably missing velocities. Is there a way to get those after
running MD?
This is my cpptraj script:
parm *.prmtop
reference *.inpcrd
trajin sim.nc
autoimage
center :1-394 mass origin
image origin center familiar
rms ToRef :1-394.CA,C,N reference out rmsd1_all.arg mass
temperature TempProt :1-394 ntc 2 out temp_prot.dat
temperature TempSolv :WAT,Cl-,Na+ ntc 2 out temp_solv.dat
go
Thank again for your help!
Best regards
Karolina
śr., 8 maj 2019 o 14:55 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
> Hi,
>
> You can use the ‘temperature’ command in cpptraj along with masks selecting
> protein/solvent to determine the temperature of each region. See the manual
> for full details.
>
> -Dan
>
> On Wed, May 8, 2019 at 2:52 AM Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I'm curious how is pmemd or sander dealing with the thermostat of the
> whole
> > system.
> > I've recently read about the hot solvent, cold solute problem and would
> > like to ask, if it is possible in either sander or pmemd to check the
> > temperature separately for the protein and the solvent?
> > And is it possible to set the thermostat separately for the protein and
> the
> > solvent?
> > How can I be sure that I'm not having a cold protein surrounded by hot
> > water?
> >
> > I'm looking forward for some more knowledge!
> > Best regards,
> > Karolina Mitusińska
> > PhD student
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> >
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Received on Wed May 08 2019 - 14:00:02 PDT
