Hi,
On Wed, May 8, 2019 at 4:33 PM Karolina Mitusińska (Markowska)
<markowska.kar.gmail.com> wrote:
>
> 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?
Oh yeah - forgot to tell you that velocities are required.
Unfortunately unless you've saved your coordinates on the order of
your time step, you can't really recover velocity info (and even then
it's not 100% correct due to the way the integrator works). You'll
have to re-run and save velocity info. Sorry for the mix-up,
-Dan
> 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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Received on Thu May 09 2019 - 11:30:02 PDT
