[gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
Neena Susan Eappen
neena.susaneappen at mail.utoronto.ca
Mon Apr 13 04:51:59 CEST 2020
Try the below minim.mdp parameters which has worked well for vacuum simulations. Proper way to do vacuum simulations: no PBC, PME and cutoffs. To reduce computation time, Konermann Lab solved it by implementing pseudo-PBC conditions. Their paper explains it very clearly (link here): https://www.ncbi.nlm.nih.gov/pubmed/29678588
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steep descent energy minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
nstxout = 100 ; Number of steps to elapse between writing coordinates to output trajectory file
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = cutoff ; Treatment of long range electrostatic interactions
rcoulomb = 333.3 ; Short-range electrostatic cut-off
vdwtype = cutoff ; Treatment of long range Van der Waals interactions
rvdw = 333.3 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
rlist = 333.3 ; short-range neighbour list cut-off
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Sunday, April 12, 2020 4:59 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
Hi Lazaro,
Please upload your minim.mdp file and potential plot say on your google drive/ one drive/ dropbox. Make it shareable and provide the link to it here. I do vacuum simulations, so I can guide you.
Neena
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se>
Sent: Sunday, April 12, 2020 3:25 PM
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Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36
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Today's Topics:
1. Re: duplicate angle index- angle restraint (Sadaf Rani)
2. Re: duplicate angle index- angle restraint (Justin Lemkul)
3. Electric field (Prithwish Nandi)
4. Re: Electric field (Prithwish Nandi)
5. how to run a MD of a small molecule in vacuum in Gromacs
(Lazaro Castanedo)
----------------------------------------------------------------------
Message: 1
Date: Sun, 12 Apr 2020 12:40:35 +0100
From: Sadaf Rani <sadafrani6 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID:
<CAH9Uu9O85zXSA5uDg_MhSFtft3XHf6fakqRAvcxMmQ3b0N1EsQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Justin
As per table 5.14 in manual, For angle restraints it selects
[image: image.png]
Also in manual under heading *Angle restraints*, it is mentioned that these
are used to restrain the angle between two pairs of particles or between
one pair of particles and the ?-axis.
Could you please correct me in setting this?
Thanks.
Sadaf
------------------------------
Message: 2
Date: Sun, 12 Apr 2020 07:44:57 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] duplicate angle index- angle restraint
Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 4/12/20 7:40 AM, Sadaf Rani wrote:
> Dear Justin
> As per table 5.14 in manual, For angle restraints it selects
>
> [image: image.png]
> Also in manual under heading *Angle restraints*, it is mentioned that these
> are used to restrain the angle between two pairs of particles or between
> one pair of particles and the ?-axis.
> Could you please correct me in setting this?
I've never used angle restraints, but clearly grompp is not expecting 4
atoms, as its error message clearly states. It is expecting to read 3
atoms, like a conventional angle.
Either there is a bug in the code or a bad description in the manual;
you'll need to look into which that is and please submit a bug report
via https://gitlab.com/gromacs
-Justin
--
==================================================
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
==================================================
------------------------------
Message: 3
Date: Sun, 12 Apr 2020 14:15:11 +0100
From: Prithwish Nandi <prithwish.nandi at ichec.ie>
To: gmx-users at gromacs.org
Subject: [gmx-users] Electric field
Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5 at ichec.ie>
Content-Type: text/plain; charset=us-ascii
Hi,
I am trying to generate an alternating e-field using gromcas input as following:
electric-field-x = 1.5 1 0 0
E0= 2 V/nm, omega = 1 cycle/ps
This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second.
I ran this input with mdrun -field option for a sanity check.
I plotted field.xvg .
Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period.
It is only 1/4 cycle of a cosine wave.
So, can you please point out what is that I am missing here?
Thanks,
PKN\\
------------------------------
Message: 4
Date: Sun, 12 Apr 2020 14:48:20 +0100
From: Prithwish Nandi <prithwish.nandi at ichec.ie>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Electric field
Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325 at ichec.ie>
Content-Type: text/plain; charset=us-ascii
Please ignore my message.
I figured it out.
It should be 2*pi*1 = 6.28 for omega to generate a full cycle.
> On 12 Apr 2020, at 14:15, Prithwish Nandi <prithwish.nandi at ichec.ie> wrote:
>
> Hi,
> I am trying to generate an alternating e-field using gromcas input as following:
>
> electric-field-x = 1.5 1 0 0
>
> E0= 2 V/nm, omega = 1 cycle/ps
>
> This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second.
>
> I ran this input with mdrun -field option for a sanity check.
>
> I plotted field.xvg .
>
> Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period.
> It is only 1/4 cycle of a cosine wave.
>
> So, can you please point out what is that I am missing here?
>
> Thanks,
>
> PKN\\
>
>
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------------------------------
Message: 5
Date: Sun, 12 Apr 2020 15:25:36 +0000
From: Lazaro Castanedo <Lazaro.Castanedo at smu.ca>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] how to run a MD of a small molecule in vacuum in
Gromacs
Message-ID:
<QB1PR01MB337802A77869BE9DEB021AB6FCDC0 at QB1PR01MB3378.CANPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future.
I have study from the manual and thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment.
But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum.
Do you think this is correct? or is correct how I am proceeding?
Should I modified the .mdp?
I am attaching the .mdp and an image of the potential energy minimization from xmgrace.
Appreciating any help in advance
kindly,
Lazaro
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