[gmx-users] weird output from simultions of a protein between two sheets
Zuzana Benkova
Zuzana.Benkova at savba.sk
Sat Apr 18 00:04:23 CEST 2020
Dear Justin,
thank you for your time. In fact, I checked the coordinates and energy values in more details. It seems that the simulation is running as it should according to the mdp parameters as the energy values indicates. The integer numbers are the rounds of real coordinates. Maybe, there is some wrong declaration of the corresponding variables in the source code.
I will report it on
https://gitlab.com/groups/gromacs/-/issues
Greetings
Zuzana
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Friday, April 17, 2020 3:21:33 PM
Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets
On 4/17/20 9:16 AM, Zuzana Benkova wrote:
> Dear Justin,
>
> thank you for your prompt response. I will answer your questions step by step.
>
> Is this just in the final coordinate file? Are coordinates in the
> trajectory correct when visualized?
>
> No, I converted all compressed trajectories to gro format and this outputs are identical in all trajectories. When I visualize the trajectory, I can see it as well. The atoms are placed in apices of boxes (1x1x1).
This is clearly a bug. Please report it on
https://gitlab.com/groups/gromacs/-/issues and include a .tpr file.
Freezing is, in any case, completely artificial and results in
collisions that do not conserve energy. Try a stiff position restraint
instead.
>
> Are you sure you don't want to remove artificial contributions to COM
> motion? This is unusual for a periodic system.
>
> I am not sure. If I leave the Linear option does the correction apply to all system even though I freeze the coordinates of graphene sheets? Anyway, I have just performed the same simulation with comm-mode = Linear and the problem persists.
The use of COM motion removal isn't directly related to your issue, but
you should still treat it properly.
-Justin
> Saving output every step is unnecessary (because you will be skewing
> your statistics with completely correlated frames) and also will
> severely degrade the performance of your simulation.
>
> Thank you for this notification. I reduce the frequency when I do equilibration and production run. I do block averages. I have saved the data every step because I tried to trace the problem.
>
> Greetings
>
> Zuzana
>
>
>
>
> ----- Original Message -----
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Friday, April 17, 2020 1:48:28 PM
> Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets
>
> On 4/17/20 7:14 AM, Zuzana Benkova wrote:
>> Dear Gromacs users,
>>
>> I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000.
>> The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK.
>> I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows
>>
>> 1GRA C1 1 0 0 0
>> 1GRA C2 2 0 0 0
>> 1GRA C3 3 0 0 0
>> 1GRA C4 4 0 0 0
>> 2GRA C1 5 0 0 0
>> 2GRA C2 6 0 1 0
>> 2GRA C3 7 0 1 0
>> 2GRA C4 8 0 1 0
>> 3GRA C1 9 0 1 0
>> 3GRA C2 10 0 1 0
>> 3GRA C3 11 0 1 0
>> 3GRA C4 12 0 1 0
> Is this just in the final coordinate file? Are coordinates in the
> trajectory correct when visualized?
>
>> my mdp parameters are as follows
>>
>> integrator = md
>> tinit = 0
>> dt = 0.001
>> nsteps = 100
>> comm-mode = None
> Are you sure you don't want to remove artificial contributions to COM
> motion? This is unusual for a periodic system.
>
>> nstcomm = 0
>> comm-grps =
>> freezegrps = Gra1 Gra2
>> freezedim = Y Y Y Y Y Y
>> energygrps = Gra1 Gra2 Protein SOL NA
>> ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 1
>> nstcalcenergy = 1
>> nstenergy = 1
>> nstxout-compressed = 1
>> compressed-x-precision = 1
> Saving output every step is unnecessary (because you will be skewing
> your statistics with completely correlated frames) and also will
> severely degrade the performance of your simulation.
>
> -Justin
>
>> pbc = xyz
>> periodic_molecules = yes
>> cutoff-scheme = Verlet
>> nstlist = 10
>> ns_type = grid
>> verlet-buffer-tolerance = 0.005
>> rlist = 1.4 ;ignored with Verlet
>> coulombtype = PME
>> coulomb-modifier = None
>> rcoulomb-switch = 1.1
>> rcoulomb = 1.3
>> vdw-type = Cut-off
>> vdw-modifier = Force-switch
>> rvdw_switch = 1.0
>> rvdw = 1.3
>> DispCorr = EnerPres
>> fourierspacing = 0.12
>> pme-order = 4
>> ewald-rtol = 1e-05
>> ewald-geometry = 3d
>> Tcoupl = V-rescale
>> nsttcouple = -1
>> tc-grps = Protein SOL_NA Gra1_Gra2
>> tau-t = 0.1 0.1 0.1
>> ref-t = 310 310 310
>> Pcoupl = no
>>
>>
>> I have to note that I got the same output with no position restraints on protein.
>>
>> Do you have any idea what the problem is?
>>
>> Thank you in advance.
>>
>> Greetings
>>
>> Zuzana
>>
>>
>>
>>
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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