[gmx-users] WHAM

[Justin Lemkul]

On 12/17/17 3:39 PM, Rose wrote:
> Why you don't answer me?is there anything wrong in my question?

Contrary to popular opinion, I don't know everything :) If I don't reply 
to a question, it is because I have nothing useful to contribute.

But since you asked, diagnosing what appears to be buggy behavior in 
wildly outdated (and unsupported, as I warned you) versions of the code 
is not a wise use of time. Upgrade to the latest version and try again.

-Justin

> Thank you
>
> Sent from my iPhone
>
>> On Dec 17, 2017, at 17:36, rose rahmani <rose.rhmn93 at gmail.com> wrote:
>>
>> Hi,
>>
>> I try to use umbrella sampling for calculating PMF. i change distance between protein and ZNS nanosheet. I use gomacsV4.5.4
>>
>> after minimization and equilibration. i use:
>>
>> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>> this is md_pull.mdp:
>> integrator               = md
>> dt                       = 0.002
>> nsteps                   = 1000000
>> nstxout                  = 5000
>> nstvout                  = 5000
>> nstfout                  = 500
>> nstlog                   = 500
>> nstenergy                = 1000
>> nstxtcout                = 1000
>> nstlist                  = 10
>> rlist                    = 1.5
>> coulombtype              = pme
>> rcoulomb                 = 1.5
>> vdwtype                  = Switch
>> rvdw_switch              = 1.0
>> rvdw                     = 1.2
>> pcoupl                   = no
>> gen_vel                  = no
>> constraints              = h-bonds
>> ns_type                  = grid
>> pbc                      = xy
>> freezegrps               = WAL ZnS
>> freezedim                = Y Y Y Y Y Y
>> energygrp-excl           = WAL WAL ZnS ZnS
>> energygrps               = SOL WAL ZnS Protein NA CL
>> nwall                    = 2
>> wall-atomtype            = C C
>> wall-type                = 9-3
>> wall-density             = 150 150
>> wall-ewald-zfac          = 3
>> ewald-geometry           = 3dc
>> fourierspacing           = 0.12
>> tcoupl                   = v-rescale
>> tc-grps                  = System
>> tau-t                    = 0.1
>> ref-t                    = 300
>> ; Pull code
>> pull                    = umbrella
>> pull_ngroups            = 1
>> pull_group0             = ZnS
>> pull_group1             = Protein
>> pull_geometry           = direction
>> pull_vec1               = 0 0 1
>> pull_dim                = N N Y
>> pull_rate1              = -0.01
>> pull_k1                 = 5000
>> pull_start              = yes
>> pull_nstxout            = 50
>>
>> then: mdrun -s pull.tpr
>> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
>>
>> i got 1000 configuration, i selected 27 of them and foe each of them i run md_umbrella.mdp
>>
>> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr and then:
>> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>>   .This is md_umbrella.mdp file:
>>
>> ntegrator               = md
>> dt                       = 0.002
>> nsteps                   = 2000000
>> nstxout                  = 5000
>> nstvout                  = 5000
>> nstfout                  = 500
>> nstlog                   = 500
>> nstenergy                = 1000
>> nstxtcout                = 1000
>> nstlist                  = 10
>> rlist                    = 1.5
>> coulombtype              = pme
>> rcoulomb                 = 1.5
>> vdwtype                  = Switch
>> rvdw_switch              = 1.0
>> rvdw                     = 1.2
>> pcoupl                   = no
>> gen_vel                  = no
>> constraints              = h-bonds
>> ns_type                  = grid
>> pbc                      = xy
>> freezegrps               = WAL ZnS
>> freezedim                = Y Y Y Y Y Y
>> energygrp-excl           = WAL WAL ZnS ZnS
>> energygrps               = SOL WAL ZnS Protein NA CL
>> nwall                    = 2
>> wall-atomtype            = C C
>> wall-type                = 9-3
>> wall-density             = 150 150
>> wall-ewald-zfac          = 3
>> ewald-geometry           = 3dc
>> fourierspacing           = 0.12
>> tcoupl                   = v-rescale
>> tc-grps                  = System
>> tau-t                    = 0.1
>> ref-t                    = 300
>>
>> pull                    = umbrella
>> pull_ngroups            = 1
>> pull_group0             = ZnS
>> pull_group1             = Protein
>> pull_geometry           = direction
>> pull_vec1               = 0 0 1
>> pull_dim                = N N Y
>> pull_rate1              = 0.0        ; 1 nm per  ns
>> pull_k1                 = 5000
>> pull_start              = yes
>> pull_nstxout            = 50
>> ...........................................................
>>
>> then i use :
>> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>>
>> i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. i don't know why?
>>
>> # This file was created Wed Dec 13 14:54:35 2017
>> # by the following command:
>> # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>> #
>> # g_wham is part of G R O M A C S:
>> #
>> # GROwing Monsters And Cloning Shrimps
>> #
>> @    title "Umbrella potential"
>> @    xaxis  label "z"
>> @    yaxis  label "E (kcal mol\S-1\N)"
>> @TYPE xy
>> 5.723834e-01    -nan
>> 6.714198e-01    -nan
>> 7.704562e-01    -nan
>> 8.694925e-01    -nan
>> 9.685289e-01    -nan
>> 1.067565e+00    -nan
>> 1.166602e+00    -nan
>> 1.265638e+00    -nan
>> .
>> .
>> .
>> .
>>
>> Would you please help me? i have not encounter this problem before
>> and also i want protein get closer to ZnS sheet during pulling in just Z direction and straightforward to sheet( like one straight line to sheet), is this suitable md_pull.mdp file for this approach? and what about time?is 4nS suitable for each window?is it possible at all?
>> Would you please help me?
>>
>> Best regards
>> Rose

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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