[gmx-users] energy group exclusion
Justin Lemkul
jalemkul at vt.edu
Sun Jan 14 23:37:26 CET 2018
On 1/14/18 12:35 PM, rose rahmani wrote:
> Yes.
> thank you so much
>
> On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/14/18 9:59 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> 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
>>> cutoff-scheme = Verlet
>>> energygrp-excl = WAL WAL ZnS ZnS
>>> coulombtype = pme
>>> rcoulomb = 1.2
>>> 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
>>> energygrps = SOL WAL ZnS Protein NA CL
>>> energygrp-excl = WAL WAL ZnS ZnS
>>> 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 = yes
>>> pull_ngroups = 2
>>> pull_ncoords = 1
>>> pull_group1_name = ZnS
>>> pull_group2_name = Protein
>>> pull_coord1_type = umbrella
>>> pull_coord1_geometry = direction
>>> pull_coord1_groups = 1 2
>>> pull_coord1_dim = N N Y
>>> pull_coord1_vec = 0 0 1
>>> pull_coord1_rate = -0.001
>>> pull_coord1_k = 5000
>>> pull_coord1_start = yes
>>> pull_nstxout = 10
>>>
>>> ----------------------------------------------
>>>
>>> ERROR 1 [file md_pull.mdp]:
>>> Energy group exclusions are not (yet) implemented for the Verlet scheme
>>>
>>>
>>> WARNING 1 [file md_pull.mdp]:
>>> Can not exclude the lattice Coulomb energy between energy groups
>>>
>>> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
>>> Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
>>> Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
>>> Note that mdrun will redetermine rlist based on the actual pair-list setup
>>> Calculating fourier grid dimensions for X Y Z
>>> Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
>>> Pull group natoms pbc atom distance at start reference at t=0
>>> 1 560 280
>>> 2 26 773 1.763 nm 1.763 nm
>>> Estimate for the relative computational load of the PME mesh part: 0.77
>>>
>>> NOTE 3 [file md_pull.mdp]:
>>> The optimal PME mesh load for parallel simulations is below 0.5
>>> and for highly parallel simulations between 0.25 and 0.33,
>>> for higher performance, increase the cut-off and the PME grid spacing.
>>>
>>>
>>> This run will generate roughly 149 Mb of data
>>>
>>> There were 3 notes
>>>
>>> There was 1 warning
>>>
>>> There were 3 notes
>>>
>>> There was 1 warning
>>>
>>> -------------------------------------------------------
>>> Program gmx grompp, VERSION 5.1.4
>>> Source code file:
>>> /home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line:
>>> 2107
>>>
>>> Fatal error:
>>> There was 1 error in input file(s)
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>>
>>> i implemented energygr-excl in mdp file, so why get this error?!
>>>
>> Read the above - such exclusions are not compatible with either the Verlet
>> scheme or with PME.
> Sorry, i couldn't understand "Read the above -such exclusions " ?
Read the messages above (error 1 and warning 1) as they tell you
precisely why things fail. Energy group exclusions are not compatible
with either Verlet or PME.
-Justin
>> and my second question is that i want to pull Protein(to get closer to
>>> sheet) to ZnS sheet, so should i use position restraint for Protein in
>>> this
>>> step?
>>>
>> If you want to induce motion in some species, does it make sense to apply
>> a biasing potential that prevents motion?
>>
>> and what is the difference between geometry= direction or distance in my
>>> system?
>>>
>> Please see the manual for a description of these features.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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