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.susaneap...@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.susaneap...@mail.utoronto.ca> > Sent: Sunday, April 12, 2020 4:59 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > gromacs.org_gmx-users-requ...@maillist.sys.kth.se < > gromacs.org_gmx-users-requ...@maillist.sys.kth.se> > Sent: Sunday, April 12, 2020 3:25 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36 > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 <sadafra...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: > < > cah9uu9o85zxsa5udg_mhsftft3xhf6fakqravcxmmq3b0n1...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Sun, 12 Apr 2020 14:15:11 +0100 > From: Prithwish Nandi <prithwish.na...@ichec.ie> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Electric field > Message-ID: <46810bf1-efc3-4e89-82c3-cb22198d3...@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.na...@ichec.ie> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Electric field > Message-ID: <61883bae-5dac-46b1-ad2d-64ee5ec34...@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.na...@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 > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > ------------------------------ > > Message: 5 > Date: Sun, 12 Apr 2020 15:25:36 +0000 > From: Lazaro Castanedo <lazaro.castan...@smu.ca> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] how to run a MD of a small molecule in vacuum in > Gromacs > Message-ID: > < > qb1pr01mb337802a77869be9deb021ab6fc...@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-us...@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 > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 36 > ****************************************************** > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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