[gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
lazaro monteserin
lamonteserincastanedo at gmail.com
Mon Apr 13 16:37:31 CEST 2020
Thank you very much Neena. I will try these parameters.
Kindly,
Lazaro
El dom., 12 de abr. de 2020 a la(s) 23:53, Neena Susan Eappen (
neena.susaneappen at mail.utoronto.ca) escribió:
> 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
> To: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> 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\\
> >
> >
> > --
> > Gromacs Users mailing list
> >
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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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