Re: [AMBER] TI residue mutation with pmemd on GPU

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Thu, 26 Sep 2019 16:33:59 +0200

Dear Premila,

I did all those things, but still the results are not good, and I cannot
find the problem. Can you take a look at the results attached? I did the
simulation three times, and you can see that It is not very obvious were is
the problem. Is it because I am using one-step transformation? Can separate
electrostatic from VdW help? Is the MBAR results from TI simulation is
AMBER good enough?

Best regards



On Thu, Sep 26, 2019 at 11:54 AM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> wrote:

> Dear Premila,
>
> I did all those things, but still the results are not good, and I cannot
> find the problem. Can you take a look at the results attached? I did the
> simulation three times, and you can see that It is not very obvious were is
> the problem. Is it because I am using one-step transformation? Can separate
> electrostatic from VdW help? Is the MBAR results from TI simulation is
> AMBER good enough?
>
> Best regards
>
>
>
>
> On Fri, Sep 20, 2019 at 3:15 PM Premila Samuel Mohan Dass <
> ps958.iqb.rutgers.edu> wrote:
>
>> 1. Try constant volume simulations (ntb=1, ntp=0);
>>
>> 2. I see you have sc as the whole residue. Prob just start from the CB
>> atoms
>>
>> 3. Work with dt=0.001
>>
>> 4. Use noshakemask for the atoms in the SC regions
>>
>>
>> Premila
>>
>> On Sep 20, 2019, at 6:18 AM, Hosein Geraili Daronkola <
>> geraili.hsn.gmail.com<mailto:geraili.hsn.gmail.com>> wrote:
>>
>> Hi all,
>> I am trying to mutate ASP to ASN on a protein using the TI one-step
>> method.
>> I have a frame from a long simulation and after heating, I am using the
>> following setup:
>> ##################################################
>> imin = 0, nstlim = 20000000, irest = 1, ntx = 5, dt = 0.002,
>> ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
>> ntc = 2, ntf = 1,
>> ntb = 2,
>> cut=12,
>> ntp = 1, pres0 = 1.0, taup = 2.0,
>> ioutfm = 1, iwrap = 1,
>> ntwe = 500, ntwx = 50000, ntpr = 500, ntwr = 500,
>> icfe = 1, ifsc = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
>> logdvdl = 0,
>> ifmbar = 1, mbar_states = %L2%,
>> mbar_lambda = %L1%,
>> timask1 = ':34', timask2 = ':130',
>> scmask1 = ':34', scmask2 = ':130',
>> /
>>
>>
>> &ewald
>> skinnb = 2,
>> dsum_tol = 1E-06,
>> /
>>
>> &wt type = 'END'
>> /
>>
>> #########################
>> windows=$(seq 0.0 0.04 1.0)
>> #########################
>>
>> I use "alchemical_analysis" to get free energy, and because the whole
>> difference that I wanna show is around 1 kcal, I need to have a low
>> standard deviation. The problem is with increasing the number of lambda to
>> 45 or increasing the simulation time, I never reach to a result with a TI
>> dhdl graph without a sharp kink, as well as a good overlapping matrix that
>> is reproducible if I do the simulation one more time, and the difference
>> between these two simulations with the same setup is bigger than one most
>> of the time. What can I change? I already increased to the point 0.01
>> distance between lambda in the sharp point, but it didn't help and there
>> are also other areas with bad overlapping matrix.
>>
>> Best
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>
>
>
>


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Received on Thu Sep 26 2019 - 08:00:01 PDT
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