Thank you for your response,
Setting mcresstr='WAT' helped, but it is not documented in manual, so I
just assumed, it is the residue name of water molecules, is it correct?
Simulation runs without errors and it is ~30 % slower so it seems mcwat
is running. However, there is almost nothing connected to mcwat in out
file except this message:
Could not find a suitable water.
Skipping monte carlo water for this iteration.
Try raising mcwatretry from 1000 if this continues.
I have no idea what mcwatretry means, can you suggest where to look for
documentation of mcwat?
Juraj
On 18. 05. 24 13:49, Carlos Simmerling via AMBER wrote:
> I haven't used mcwat very much, so others may be able to offer more help.
> Hopefully these will be useful:
> I would start by making sure your mcat setup works in standard MD before
> trying to combine with TI.
> also, I usually put commas after all variable definitions.
> try defining mcresstr
>
>
> On Fri, May 17, 2024 at 3:24 PM Juraj Dobias via AMBER <amber.ambermd.org>
> wrote:
>
>> Hi,
>>
>> I wanted to use Monte Carlo water equilibration
>> (https://pubs.acs.org/doi/10.1021/acs.jctc.1c00867) to sample buried
>> water molecules in my RBFE calculation. My input settings are:
>>
>> &cntrl
>> nstlim = 250000, dt = 0.002000,
>> imin = 0
>> ntxo = 1
>> ntc = 2
>> ntf = 1
>> cut = 10
>> iwrap = 1
>> ntt = 3
>> gamma_ln = 2.0
>> ntpr = 5000
>> ntwr = 50000
>> mcwat=1
>> nmd = 1000
>> nmc = 100000
>> mcwatmask = ':L1'
>> mcligshift = 12
>> irest = 1, ntx = 5
>> barostat=2, ntp=1, taup=2
>> ntwx=10000
>>
>> clambda=0.000000
>> ifsc = 1
>> icfe = 1
>> scalpha = 0.5
>> scbeta = 1.0
>> gti_add_sc = 5
>> gti_scale_beta = 1
>> gti_cut_sc_on = 8
>> gti_cut_sc_off = 10
>> gti_lam_sch = 1
>> gti_ele_sc = 1
>> gti_vdw_sc = 1
>> gti_cut_sc = 2
>> gti_ele_exp = 2
>> gti_vdw_exp = 2
>> gti_syn_mass = 0
>> scmask1 = ':L1&(@H14)'
>> scmask2 = ':L2&(.C17,O3,N5,H14,H15)'
>> timask1 = ':L1'
>> timask2 = ':L2'
>> noshakemask = ':L1,L2'
>> /
>>
>> Simulation stopped with error:
>>
>> Error in definition of mcres - residue with name does not exist.
>>
>> I am pretty sure that my mcwatmask is valid. Simulation with mcwat=0 is
>> running without issues.
>>
>> Any help would be appreciated.
>>
>> Juraj Dobias
>>
>>
>>
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Received on Sat May 18 2024 - 12:00:02 PDT
