mdin file:
&cntrl
imin=0, irest=0, ntx=1,
ntt=3, gamma_ln=2.0, temp0=310.0, tautp=1.0,
ntc=2, ntf=2, ntb=2, ntp=1, pres0=1.0, taup=1.0, barostat=2
cut=10.0, iwrap=1, ig=-1,
ntpr=1, ntwr=1, ntwx=1,
nstlim=200000, dt=0.002,
ioutfm=1, nmropt=1,
/
&wt type='DUMPFREQ', istep1=1 /
&wt type='END' /
DISANG=nmr
DUMPAVE=dist_vs_t
cpptraj command:
distance d1 :178.N,C8,C9,C10 :179.N,C8,C9,C10 out test.dat
one of nmr restraint files:
&rst iat=-1,-1,0
r1=10.000000, r2=20.000000, r3=21.000000, r4=21.500000, rk2=10.000000, rk3=0.000000,
IGR1(1)=2813,IGR1(2)=2815,IGR1(3)=2817,IGR1(4)=2821,
IGR2(1)=2860,IGR2(2)=2862,IGR2(3)=2864,IGR2(4)=2868,
nstep1=0, nstep2=0,
&end
MD with the above conditions initially produced same distance (indicating that the atom index is correct in cpptraj and in IGR) in dist_vs_t and test.dat until thousands of steps of simulation when the distance in dist_vs_t and test.dat are different.
Is there anything wrong with my control file?
Thanks,
Ming
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Tuesday, 23 March 2021 8:35 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
Hi Ming,
can you include your mdin file and also the cpptraj script? then people
will be able to see what you're doing.
On Tue, Mar 23, 2021 at 12:31 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> Hey Carlos,
>
> Thanks for your suggestion. The system shows the restraint is working as
> two compounds initially closer than r2 angstroms were pulled away from each
> other until they are more than r2 angstroms away due to the repulsive
> force. But after the simulation goes on for a while, some compounds do not
> repel each other even if there are close to each other. I extracted the
> distance between two restrained groups from the output file generated by
> DUMPAVE and calculated the distance via cpptraj distance command.
> Initially, their values are same because the two molecules are in the same
> box, but after a while (the length of the time depends on the selected
> groups and the simulation), their values are different, e.g., the distance
> calculated from distance command is smaller than r2, whereas the distance
> from DUMPAVE is much larger than r2. Therefore, the two close groups are
> not restrained. I have been outputting and calculating the distance per 1
> step, and after restart the simulation multiple times, I came across the
> above same issue. I am totally not sure what is wrong here.
>
> Thanks,
> Ming
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, 19 March 2021 1:05 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
>
> I would not think about what happens after autoimage- that's not what is
> going on in your simulation and the restraints will only be applied to what
> happens during MD.
> focus on the input structure that you give to sander or pmemd, and whether
> you use imaging during MD or not. also on how you set up the pairs and
> distances for the restraints.
> can you simplify the problem to a single restraint that you think isn't
> working, and explain what your restraint is, the initial coordinates for
> that pair, and why you think it isn't working during MD?
>
>
>
> On Thu, Mar 18, 2021 at 10:53 AM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> > Yes. I tried both iwrap=0 and 1, and the distance is same and not real
> > (not equal to the distance after the cpptraj autoimage process)
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Thursday, 18 March 2021 8:35 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
> >
> > what do you mean by "before autoimage"? autoimage is a cpptraj command,
> but
> > it sounds like you are talking about what happens in the MD run.
> > do you have iwrap=1 in your simulation?
> >
> >
> > On Thu, Mar 18, 2021 at 12:15 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> >
> > > Dear Carlos and David,
> > >
> > > Thank you very much for your guidance. Yes, I found that a positive rk2
> > > does the right thing and the problem lies in how the system calculates
> > the
> > > distance between two IGRs. I found out that the system calculates the
> > > distance based on the coordinate before autoimage, and therefore the
> > small
> > > molecules do not get close in the trajectory before the autoimage
> > process.
> > > I guess this comes from the periodic boundary condition setting.
> > >
> > > Is there a way to fix this?
> > >
> > > Many thanks,
> > > Ming
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > > Sent: Tuesday, 16 March 2021 11:41 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] Apply Lennar-Jones potential between small
> molecules
> > >
> > > On Tue, Mar 16, 2021 at 8:56 AM David A Case <david.case.rutgers.edu>
> > > wrote:
> > >
> > > > On Tue, Mar 16, 2021, Carlos Simmerling wrote:
> > > >
> > > > >yes negative rk gives an inverted parabola, so it is repulsive if it
> > is
> > > > >outside the flat region.
> > > >
> > > > I'm a little confused here, and would recommend careful testing if
> you
> > > are
> > > > setting rk2 to a negative number. I've not done that but it *sounds*
> > > > dangerous. Probably a good idea to numerically plot the function vs.
> > > > distance, and make sure you are getting the behavior you want.
> > > >
> > > >
> > > Dave is right, this can be really dangerous since it goes to infinitely
> > > negative energies. I've used it and technically it does work, but it's
> > > probably much safer to use other options. I should have been more
> careful
> > > in giving caution along with my reply!
> > >
> > > re-reading the original question, a negative rk2 will make them
> > ATTRACTIVE
> > > below r2, and it doesn't sound like this is what you want. *For
> repulsive
> > > interaction below r2 you want a positive rk2.*
> > > _______________________________________________
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> > >
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Received on Tue Mar 23 2021 - 16:30:02 PDT
