That energy change with shake is unusual - were your endpoints equolirbated
without shake prior to the NEB run?
On Tue, Nov 19, 2019, 9:51 AM Madhur Aggarwal <
madhur.aggarwal.research.iiit.ac.in> wrote:
> Hi Delaram,
>
> I could not stop the end states from moving with skmin, skmax=1.
> But, I repeated the entire procedure again from start and I could stop the
> end states from moving in case of both implicit and explicit solvent by
> taking ntc, ntf=1, as in Alanine dipeptide tutorial (taking skmin, skmax=10
> itself). I believe the SHAKE algorithm when called forces the H-atoms to
> achieve their equilibrium bond lengths, even though NEB does not allow
> that, which somehow was causing the increment in potential energy (but if
> bonds are reaching their equilibrium length, energy should decrease!) of
> the end states and change in conformation. As you said, this change just
> happens from step1 to step2 in loop of MD and not after that.
> In my case, I can allow H-atoms to move, so my problem is solved. But, you
> may want to look into why this is happening.
>
> Thanks once again for your time and valuable inputs,
> Madhur Aggarwal
> ------------------------------
> *From:* Ghoreishi, Delaram <delaram.phys.ufl.edu>
> *Sent:* Tuesday, November 19, 2019 12:25 PM
> *To:* Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>; AMBER
> Mailing List <amber.ambermd.org>
> *Cc:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Subject:* Re: [AMBER] Conformation of NEB end states changing during
> 1HEAT
>
>
> Dear Madhur,
>
>
> The end-state coordinate update in the cuda NEB code happens from step 1
> to 2 in the loop of the molecular dynamics. Afterward, the end-state
> replicas remain fixed. I was aware of this behavior when I was writing the
> code, but I did not invest much time on it (this has been sitting in my
> TODO list for some time!). However, updating the coordinates once does not
> do any damage. The results you would get from performing NEB would still be
> correct and statistically equivalent to the previous implementation.
>
>
> So, the reason your simulations are failing is not that. I believe if you
> pick a smaller spring constant (skmin, skmax = 1) at the initial stage
> where you superimpose the NEB replicas, your simulations would finish
> successfully.
>
>
> Let me know if you were able to make it work.
>
>
> -Delaram
>
>
> ------------------------------
> *From:* Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
> *Sent:* Monday, November 18, 2019 2:44 PM
> *To:* AMBER Mailing List
> *Cc:* Ghoreishi, Delaram; Carlos Simmerling
> *Subject:* Re: [AMBER] Conformation of NEB end states changing during
> 1HEAT
>
> *[External Email]*
> Hi Delaram, Carlos,
>
> Thank you for your prompt reply.
> As per Carlos's suggestion, I am focussing on NEB calcs in implicit
> solvent only for Alanine dipeptide (attached ala_implicit.1heat.sh) and
> my system for now ..
> I compared the 2 mdin scripts line by line and I realized that there was
> one difference .. I had put SHAKE constraints on hydrogen atoms in my
> system, which were not there in case of Alanine dipeptide. I removed these
> constraints (attached modified implicit.1heat.sh) and ran simulation once
> again on my system.
> For my system, by looking at the mdout file (attached mysys.neb.out.000),
> I see that the energies for end states change by a very small amount (in
> decimals) when their values are compared at NSTEPS=0 and NSTEPS=500 ..
> energy values for the end states remain constant after that ..
> Whereas in the case of Alanine dipeptide, the energy values seem to remain
> constant throughout, upto 3 decimal places. (attached ala.neb.out.000).
> When I compare the PDB files of the initial and final conformations of
> each end state, the coordinates differ. (Attached initial and final pdb
> files for one of my end state state1 here).
>
> .Delaram, I have attached state1.prmtop, state1.inpcrd (after
> minimization) and state2.inpcrd (after minimization) files here.
>
> Thanks a lot for your time,
> Madhur Aggarwal
>
> ------------------------------
> *From:* Madhur Aggarwal <madhur.aggarwal.research.iiit.ac.in>
> *Sent:* Tuesday, November 19, 2019 1:10 AM
> *To:* AMBER Mailing List <amber.ambermd.org>; Ghoreishi, Delaram <
> delaram.phys.ufl.edu>; Carlos Simmerling <carlos.simmerling.gmail.com>
> *Subject:* Re: [AMBER] Conformation of NEB end states changing during
> 1HEAT
>
> Hi Delaram, Carlos,
>
> Thank you for your prompt reply.
> As per Carlos's suggestion, I am focussing on NEB calcs in implicit
> solvent only for Alanine dipeptide (attached ala_implicit.1heat.sh) and
> my system for now ..
> I compared the 2 mdin scripts line by line and I realized that there was
> one difference .. I had put SHAKE constraints on hydrogen atoms in my
> system, which were not there in case of Alanine dipeptide. I removed these
> constraints (attached modified implicit.1heat.sh) and ran simulation once
> again on my system.
> For my system, by looking at the mdout file (attached mysys.neb.out.000),
> I see that the energies for end states change by a very small amount (in
> decimals) when their values are compared at NSTEPS=0 and NSTEPS=500 ..
> energy values for the end states remain constant after that ..
> Whereas in the case of Alanine dipeptide, the energy values seem to remain
> constant throughout, upto 3 decimal places. (attached ala.neb.out.000).
> When I compare the PDB files of the initial and final conformations of
> each end state, the coordinates differ. (Attached initial and final pdb
> files for one of my end state state1 here).
>
> .Delaram, I have attached state1.prmtop, state1.inpcrd (after
> minimization) and state2.inpcrd (after minimization) files here.
>
> Thanks a lot for your time,
> Madhur Aggarwal
>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Monday, November 18, 2019 11:10 PM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Conformation of NEB end states changing during
> 1HEAT
>
> I'm a little confused about what's happening. you say that alanine
> dipeptide works fine in implicit solvent, but your system does not work
> fine in implicit solvent? if so, then for now let's ignore explicit solvent
> since you have 2 setups to compare, and one works while the other does not.
> did you compare line by line the input file for your system vs the one you
> used for the dipeptide that worked? you didn't include the working example
> here so we can't test that. you also want to compare the run scripts, not
> just the mdin files. something must not be the same.
> it can also help to carefully look at the mdout files and make sure it is
> doing what you think it should. again, you have a working example and a
> non-working example, so you can compare them.
>
> On Mon, Nov 18, 2019 at 12:10 PM Madhur Aggarwal <
> madhur.aggarwal.research.iiit.ac.in> wrote:
>
> > Hi all,
> >
> > I am using Amber18 to run NEB simulations on my protein + water system. I
> > minimized both the end states and made sure the prmtop file generated is
> > the same for both the end states. Then, I am following Tutorial A5 on NEB
> > calcs on Alanine dipeptide.
> > The issue is when I run step 4 to generate images and heat the system, my
> > end states are also undergoing a change in their conformation, which
> should
> > not happen (attached explicit.1heat.sh).
> > When I try doing the calculations on Alanine dipeptide in implicit
> solvent
> > (as done in the tutorial), it works fine. So, I thought maybe it has
> > something to do with my explicit solvent. But when I do the calculations
> on
> > my system using implicit solvent, the conformations of my end states are
> > still changing (attached implicit.1heat.sh).
> > I am not able to figure out why this is happening. I would really
> > appreciate if someone could help me out with this. I have attached my
> input
> > scripts for both implicit and explicit solvent cases here.
> >
> > Thanks,
> > Madhur Aggarwal
> > _______________________________________________
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> > AMBER.ambermd.org
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Received on Tue Nov 19 2019 - 08:00:02 PST
