Hi Daniel,
Thank you very much for your guidance.
Yes, unwrap and noimage make the distances match each other. Does this mean that distance restraint on different compounds cannot used together with periodic bounds conditions? Is there any other ways in amber that can apply distance restraint on small molecules to prevent them from aggregating?
Many thanks,
Ming
-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, 24 March 2021 11:48 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
Hi,
On Tue, Mar 23, 2021 at 7:21 PM Ming Tang <m21.tang.qut.edu.au> wrote:
> 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.
To understand this, you need to understand how imaging works in Amber.
During the MD simulation, imaging (when iwrap=1) applies *only* to the output trajectory, i.e. molecules are not actually "wrapped" when they cross the unit cell boundary. So things like restraint distance do
*not* use the minimum image convention. This is why it is important to use 'autoimage' on input coordinates prior to restarting a simulation of multiple molecules with restraints - if one of the molecules was imaged, the restraint distance will not account for that.
However, by default the 'distance' action in cpptraj *does* use the minimum image convention. So I'm guessing what happens is in the simulation, one of the molecules crosses a unit cell boundary. To test this, calculate the distance again with cpptraj, but this time use the 'unwrap' action followed by 'distance' with the 'noimage' keyword, e.g.
unwrap
distance d1 :178.N,C8,C9,C10 :179.N,C8,C9,C10 out test.dat noimage
I'm guessing the two distances will then match.
The long-term solution here is to use 'iwrap=0' (i.e. no imaging) when you have NetCDF trajectory/restarts enabled. I think we need to start making this the default behavior in Amber to avoid imaging issues.
-Dan
>
> 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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Received on Wed Mar 24 2021 - 16:00:02 PDT
