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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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Received on Mon May 04 2020 - 06:30:03 PDT
