[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 95
Seketoulie Keretsu
sekekeretsu at gmail.com
Tue Nov 27 07:33:53 CET 2018
Dear Alex
Thank you for the "shameless self promotion". Have been looking for
some classic gromacs products lately. Have seen some interesting
methods in area of protein-ligand interactions. If you have some new
and interesting gromacs papers related to Protein-ligand studies
please suggest it here.
Also came across this paper out of Stanford university. 400 micro sec
simulations. Just blown my mind.
https://www.nature.com/articles/s41467-016-0015-8
Will really appreciate if you can suggest .
Appreciate you guys for all the help so far.
Best, Seke
On Tue, Nov 27, 2018 at 1:05 PM
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Parameterizing N-terminal capping (Raji)
> 2. Re: Distance calculation (rose rahmani)
> 3. Re: Interaction energy (Mark Abraham)
> 4. shameless self-promotion (Alex)
> 5. Gromacs 2018.3 Exceeding Memory Issue (Peiyin Lee)
> 6. Re: Charge system simulation problem (Karpurmanjari Kakati)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 26 Nov 2018 12:50:05 -0600
> From: Raji <raji.phy at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Parameterizing N-terminal capping
> Message-ID:
> <CAPoAzqqkj_PP=_8ouWsSf1pB2VBdbR_EMsa=hgKgrGG_q9sNwA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi
>
> I am trying to parameterize the N-terminal ?carboxybenzyl? capping for
> peptide within CHARMM force field. Charges and bonded terms are transferred
> by analogy from available amino acid and lipid parameters. Grompp throwing
> errors for missing dihedral and bond terms of the linkage between ester
> group and peptide backbone. I appreciate any ideas.
>
>
> [image: image.png]
> Thanks
> Raji
>
> ------------------------------
>
> Message: 2
> Date: Mon, 26 Nov 2018 22:29:07 +0330
> From: rose rahmani <rose.rhmn93 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Distance calculation
> Message-ID:
> <CAO6==5TQ_vOrJKi+SroYzmFDCHVMHkdu74Ah-QboFMrmYu4L4w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Can i use -dist option?
> Would you please help me?
> On Mon, 26 Nov 2018, 00:48 rose rahmani <rose.rhmn93 at gmail.com wrote:
>
> > Hi,
> >
> > My system contains 20 amino acids around nanotube. I want to know the
> > adsorption amount of AA during simulation time; the adsorption occurs
> > when the distance between one of non-hydrogen atoms of AA and the tube
> > surface was less than 0.5 nm. So how can i calculate this property?
> >
> > Would you please help me?
> > Best
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 26 Nov 2018 21:51:50 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Interaction energy
> Message-ID:
> <CAMNuMAQbgCiLQNXkCmcuZNe=mBYQSLm4MS=4oeuJ9OjXW42_gQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> On Mon, Nov 26, 2018 at 7:47 PM Nick Johans <johans.nick93 at gmail.com> wrote:
>
> > On Mon, 26 Nov 2018, 21:28 Justin Lemkul <jalemkul at vt.edu wrote:
> >
> > >
> > >
> > > On 11/26/18 10:51 AM, Nick Johans wrote:
> > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul <jalemkul at vt.edu wrote:
> > > >
> > > >>
> > > >> On 11/22/18 11:41 AM, Nick Johans wrote:
> > > >>> Hi
> > > >>>
> > > >>> I am beginner in MD. Maybe it is not a wise question but i want to
> > > >>> calculate the interaction energy between protein and ligand and also
> > > PMF
> > > >> in
> > > >>> different distances. But i don't know what is the didference between
> > > >> PMF, i
> > > >>> mean free energy in particular(by umbrella sampling) and the
> > > interaction
> > > >>> energy (by g_energy tool) in my case?
> > > >> Interaction energy is a pairwise decomposition of short-range
> > nonbonded
> > > >> interaction energy in the system. This energy is usually not
> > physically
> > > >> meaningful, but if the force field has been parametrized in such a way
> > > >> that it is, the interaction energy is a contribution to the enthalpy
> > of
> > > >> the system.
> > > >>
> > > > What forcefields embedded in GROMACS do, yes?
> > >
> > > AFAIK only CHARMM.
> > >
> > Interesting! You mean interaction energy calculated by for example AMBER
> > may not be true? Why?? What makes CHARMM unique??
> >
>
> As Justin said, the difference is in the way it is parametrized.
> Forcefields are generally built to be additive, but it does not follow that
> they are decomposable.
>
> > > If coulomb energy is also existed between pairs, so the interaction
> > > energy
> > > > will be LJ+Coulomb yes?
> > >
> > > Pairs are 1-4 (intramolecular) interactions, so if you define
> > > interaction energy between two nonbonded species, you'll get zeroes for
> > > all the pair energies, by definition.
> > >
> > It's exactly the SR(short range) selection in g_energy, yes?
>
>
> You seem to be using a looser definition of pairs than is usual in
> discussion of GROMACS topologies.
>
>
> > all long range
> > are zero.
>
>
> If there's a long-range model, then such interactions are not uniformly of
> zero magnitude...
>
>
> > But coulomb and LJ are non-zero. So, in this case the interaction
> > energy would be
> > Short range LJ+ Short range Coulomb , true?
> >
>
> As far as I'm concerned, you can invent whatever quantity you want, but the
> burden is on you to demonstrate that there's a reason to connect it to
> something physical.
>
> Mark
>
>
> > >
> > > > So what about PMF. It seems like an interaction energy too, but more
> > > > accurate one???
> > >
> > > That's not what a PMF is. A PMF is the change in free energy of a system
> > > as a function of progress along a reaction coordinate.
> > >
> > > -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
> > >
> > > ==================================================
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > >
> > --
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>
> ------------------------------
>
> Message: 4
> Date: Mon, 26 Nov 2018 14:20:21 -0700
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] shameless self-promotion
> Message-ID:
> <CAMJZ6qEiq82JdEn8sQf0LJkwkaHuwVJ+ZQHe09RLBn68HoJpPQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> This isn't a Gromacs question, but a bit of self-promotion with a
> not-so-hidden agenda.
>
> 1. Here's our paper that I think might be of interest to you beautiful
> biophysics folks: https://www.nature.com/articles/s41563-018-0220-4
>
> 2. All of this was done with Gromacs. I cannot imagine any other package
> capable of providing simulated timescales like this without an actual
> supercomputer (we had three GPU-accelerated nodes). We use other MD
> packages (which will not be named) and nothing comes close speed-wise. Our
> endless love and gratitude go to the developers.
>
> 3. GMX developers: We will _NOT_ stop using Gromacs for non-biomolecules!
> It can be done and it should be done, and Gromacs works for these systems.
> Sometimes with a little bit of system design pain, but it does. Maybe one
> day you will find it in your hearts to listen to the solid-state folks and
> start extending software capabilities to meet our needs more directly. One
> can only hope. ;)
>
> I invite your "wow that's interesting stuff" and other comments here.
> Again, thanks!
>
> Alex
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 26 Nov 2018 22:30:18 -0500
> From: Peiyin Lee <peiyinlee329 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Gromacs 2018.3 Exceeding Memory Issue
> Message-ID:
> <CAPd-doghozLg+L13sqVxCc2iJ3MK5ETuuNDegEZ4PRcmY5p2RQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi, all GROMACS users,
>
> I am trying to run jobs with Gromacs 2018.3 version and constantly got a
> memory exceeding error. The system I ran is an all-atom system with 21073
> atoms. The largest file that is estimated to be generated is around 5.8 GB.
> My jobs got constantly killed after running for only around 15 minutes and
> got an error message like this: "slurmstepd: error: Job 12381762 exceeded
> memory limit (123122052 > 122880000), being killed". I have tried using a
> larger memory specification (12GB/core) but it would take too long to wait
> and I don't think my job really uses that many memories. I have attached my
> .mdp file as below:
> "title = NVT Production Run for Trpzip4 in pure H2O
>
> define = ; position restrain the protein
>
> ; Run parameters
>
> integrator = md ; leap-frog integrator
>
> nsteps = 50000000 ; 0.002 * 50000 = 100000 ps (100 ns)
>
> dt = 0.002 ; 2 fs
>
> ; Output control
>
> nstenergy = 10000 ; save energies every 20 ps
>
> nstlog = 10000 ; update log file every 20 ps
>
> nstxout-compressed = 10000 ; 20ps
>
> compressed-x-precision = 200 ; 0.05
>
> compressed-x-grps = System
>
> ; Bond parameters
>
> continuation = yes ; Restarting after NVT
>
> constraint_algorithm = lincs ; holonomic constraints
>
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
>
> lincs_iter = 1 ; accuracy of LINCS
>
> lincs_order = 4 ; also related to accuracy
>
> ; Neighborsearching
>
> ns_type = grid ; search neighboring grid cels
>
> nstlist = 5 ; 10 fs
>
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
>
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>
> pme_order = 4 ; cubic interpolation
>
> fourierspacing = 0.16 ; grid spacing for FFT
>
> ; Temperature coupling is on
>
> tcoupl = V-rescale ; More accurate thermostat
>
> tc-grps = Protein SOL NA ; 2 coupling groups - more accurate
>
> tau_t = 0.5 0.5 0.5 ; time constant, in ps
>
> ref_t = 400 400 400 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is on
>
> pcoupl = No ; Pressure coupling on in NPT
>
> pcoupltype = isotropic ; uniform scaling of x-y box vectors,
> independent z
>
> tau_p = 5.0 ; time constant, in ps
>
> ref_p = 1.0 ; reference pressure, x-y, z (in bar)
>
> compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
>
> ; Periodic boundary conditions
>
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = no ; Velocity generation is off"
> and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
> -noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo md.cpt
> -g md.log". This is my first time posting so please excuse anything that's
> unclear. I will try to clarify if needed. Any help is greatly appreciated!
>
> Regards,
> Peiyin Lee
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 27 Nov 2018 09:32:59 +0530
> From: Karpurmanjari Kakati <ch18resch01002 at iith.ac.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se, gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charge system simulation problem
> Message-ID:
> <CALYmPE+dHjjgfqkUSaAbMLQRi7dFSi9su7jciBs23NevfqtaMA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Justin,
>
> Because I have self generated the itp file, and that's the only place where
> charge in terms of partial charge is added. Is the problem lying there?
> Also can't we denote the partial charges in decimal because in real some
> atoms will have net charges that can be decimal values due to presence or
> absence of electronegative atoms adjacent to it?
>
>
> And are all the other notes and warnings generated are all because of that?
>
>
> karpurmanjari
>
> On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <
> ch18resch01002 at iith.ac.in> wrote:
>
> > Dear All,
> >
> > My System contains, while doing NVT of the same, I got the following Note
> >
> >
> >
> >
> >
> >
> > *NOTE 1 [file sa.top, line 80]: System has non-zero total charge:
> > 12.936997 Total charge should normally be an integer. See
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> for
> > discussion on how close it should be to an integer.*
> >
> >
> > This is possibly because of the partial charges in the molecules in the
> > ITP fie.
> > My doubt is can't I have a system with non zero and a decimal charge value.
> >
> >
> > Also I got the following warning:
> >
> >
> >
> >
> >
> >
> > *WARNING 1 [file sa.top, line 80]: You are using Ewald electrostatics in
> > a system with net charge. This can lead to severe artifacts, such as ions
> > moving into regions with low dielectric, due to the uniform background
> > charge. We suggest to neutralize your system with counter ions, possibly
> > in combination with a physiological salt concentration.*
> >
> > Can Someone help me with this?
> >
> > Also this :
> >
> >
> >
> >
> >
> >
> >
> > *Velocities were taken from a Maxwell distribution at 300 KRemoving all
> > charge groups because cutoff-scheme=VerletAnalysing residue names:There
> > are: 1 Other residuesThere are: 100000 Water residues*
> >
> >
> > Removing all charge group because the cut off scheme is verlet.
> >
> > If That happens then will it show the behavior I want to see. Or shall I
> > put any other scheme on that ?
> >
> > Please help
> >
> >
>
>
> ------------------------------
>
> --
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> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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