I think you may need to reach out to GROMACS users for help on this.
On Mon, May 4, 2020 at 9:08 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
> Dear Carlos
> I have worked with removing charges alone before doing calculations for
> Vdw. Charge removal calculations work well till 10ns.
> Please find the files in the link below:-
>
> https://www.dropbox.com/sh/da0e1ueupokazhr/AAAB6HRUHtDqu7y4rWuxwirQa?dl=0
>
> I am getting the following output for the error for Vdw run.
> starting mdrun 'GROtesk MACabre and Sinister in water'
> 1000000 steps, 1000.0 ps.
>
> Step 853159, time 853.159 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000569, max 0.041969 (between atoms 3430 and 3439)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 3435 3437 38.0 0.1400 0.1415 0.1400
> 3437 3438 52.2 0.1080 0.1068 0.1080
> 3437 3439 39.0 0.1400 0.1402 0.1400
>
> Step 853159, time 853.159 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000550, max 0.040414 (between atoms 3430 and 3439)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 3435 3437 37.8 0.1400 0.1415 0.1400
> 3437 3438 51.9 0.1080 0.1070 0.1080
> 3437 3439 38.6 0.1400 0.1403 0.1400
>
> Step 853160, time 853.16 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000833, max 0.054713 (between atoms 3437 and 3438)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 3430 3439 30.5 0.1457 0.1428 0.1400
>
> Your suggestion would really help to fix the problem.
>
> Thanks.
>
> Sadaf
>
>
>
>
>
>
> On Sun, May 3, 2020 at 1:29 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
>
> > Dear Carlos
> > I am following the paper
> > https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467
> > yes, I have removed charge on the system before removing the vdw and
> > keeping the one distance, two angles, and three dihedral restraints on as
> > mentioned in the reference paper. During decoupling, I have softcore
> > potentials in my simulation.
> > I would be really grateful for your help in fixing this problem I am
> > facing since long.
> >
> > Thanks.
> >
> > Sadaf
> >
> >
> >
> > On Sun, May 3, 2020 at 12:45 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> Have you already removed the charge on the atoms for which you are
> >> removing
> >> vdw? Also, there can be a discontinuity at endpoints, so many
> researchers
> >> do not fully disappear atoms. Are you following the method in a specific
> >> paper? Another option is to use a soft core treatment. Since we know
> very
> >> little about how you are doing the perturbation it is difficult to help.
> >>
> >> On Sat, May 2, 2020, 6:54 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
> >>
> >> > Dear Amber users
> >> > Although this forum is for the problems related to Amber only and I am
> >> > using gromacs for the moment, but I want to get your expert advice on
> >> > the topic other than software. I also tried on the research gate but
> >> could
> >> > not get any reply. I assume people here are experts in this area of
> >> > research as well that's why I am posting my question to get an
> >> > understanding of my problem.
> >> > currently, I am I have a protein-ligand system for which I am doing TI
> >> > calculation. During vdw removal, my system crashes and generates
> >> different
> >> > PDB structures. It is assumed that this normally happens when the
> >> system is
> >> > not well equilibrated however, I have a well-equilibrated system. I
> also
> >> > reduced the time step to 1 fs but still the same problem when the
> lambda
> >> > window gets closer to 1. I tried with h-bond constraints as well as
> with
> >> > all bonds constraint but still could not solve the problem. My system
> >> gives
> >> > lincs warning and then crashes.
> >> > Could you please give some suggestions what else could I look for in
> my
> >> > system to solve this problem.
> >> >
> >> > Thanks in advance.
> >> >
> >> > Sadaf
> >> > _______________________________________________
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> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
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> >>
> >
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Received on Mon May 04 2020 - 06:30:03 PDT
