[gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 117
sunita gupta
sunita.bio at gmail.com
Tue Nov 26 14:09:13 CET 2013
Thanks Justin,
Its strange that some atomtypes like ha, h1, n2 etc whose parameters are
already present in the gbsa.itp are also not recognised.
I have many more ligands to deal with. Can you tell me how to overcome this
issue, or whats the possibility of doing implicit simulation of
protein-ligand complexes with gromacs
Thanks
On Tue, Nov 26, 2013 at 6:17 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Coulombic potential modifiers in Gromacs 4.6.4. (Mark Abraham)
> 2. Re: GPU g_energy problem (Justin Lemkul)
> 3. Re: Can't do GB electrostatics; the implicit_genborn_params
> section of the forcefield is missing parameters for 9 atomtypes
> or they might be negative. (Justin Lemkul)
> 4. Re: (no subject) (Justin Lemkul)
> 5. Fwd: Can't do GB electrostatics; the implicit_genborn_params
> section of the forcefield is missing parameters for 9 atomtypes
> or they might be negative. (sunita gupta)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 Nov 2013 12:40:49 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Coulombic potential modifiers in Gromacs
> 4.6.4.
> Message-ID:
> <
> CAMNuMATYEkUceKjekSA-LP3Kti5JWTE645nrSO39DftSsFo8oA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Nov 22, 2013 5:58 PM, "rajat desikan" <rajatdesikan at gmail.com> wrote:
> >
> > Hi Mark,
> >
> > Thanks for the answer. I have a few doubts.
> >
> > 1) "The whole potential is shifted by the value that it would otherwise
> > have had at the cut-off." Doesn't this reduce the well-depth/epsilon for
> > the LJ potential (same artifact as shifted LJ)?
>
> Yup, but is this more important than the alternative problem?
>
> > Will the long range
> > corrections/DispCorr correct for this?
>
> Good question, I don't know. Would be easy to do two single-points and
> compare the energies and forces.
>
> > 2) "This is cosmetic in MD, unless you plan to compute based upon the
> > energies." I am not very clear on this. Are there situations when I
> should
> > not be using this? I can understand that shifted potentials cause
> > difficulties in sensitive cases like near gas-liquid critical points,
> etc.
> > Are there bio-molecular situations that one should be cautious about?
>
> I don't know the work to which you refer, but the point in MD is that one
> does not even need to compute the energy every step (and GROMACS does not,
> unless nstcalcenergy is 1). Evolution proceeds via the forces. However,
> certain algorithms do have ways for energies to affect the sampling, or
> perhaps post hoc through reweighting algorithms. Whether the jitter in VDW
> energies as particles move across an unswitched VDW cutoff is significant
> for these is another matter.
>
> > 3) How would these modifiers affect the simulation in the presence of an
> > external electric field?
>
> The LJ? Not at all ;-)
>
> Mark
>
>
> > Thanks, I appreciate your time. The manual did not have the answers I
> need.
> >
> >
> > On Fri, Nov 22, 2013 at 10:03 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
> >
> > > On Nov 21, 2013 9:20 AM, "rajat desikan" <rajatdesikan at gmail.com>
> wrote:
> > > >
> > > > Hi All,
> > > >
> > > > I was wondering about the coulomb-modifier = Potential-shift-Verlet
> > > option
> > > > in conjunction with the Verlet cut-off scheme and PME.
> > > >
> > > > I can understand that vdw-modifier = Potential-shift-Verlet shifts
> the
> > > > truncated LJ tail by a constant so that the potential is the integral
> of
> > > > the force.
> > >
> > > No, see http://manual.gromacs.org/online/mdp_opt.html#el. The whole
> > > potential is shifted by the value that it would otherwise have had at
> the
> > > cut-off. This is cosmetic in MD, unless you plan to compute based upon
> the
> > > energies. Whether something else is trying to compensate for the
> missing
> > > long-range interactions has nothing to do with it.
> > >
> > > Mark
> > >
> > > > What does the coulomb-modifier do? We are accounting for the
> > > > long range coulombic interactions using reciprocal space sums in PME,
> > > > right? What exactly is the shift here?
> > > >
> > > > Thanks
> > > >
> > > > --
> > > > Rajat Desikan (Ph.D Scholar)
> > > > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > > > Dept. of Chemical Engineering,
> > > > Indian Institute of Science, Bangalore
> > > > --
> > > > 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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> > > --
> > > Gromacs Users mailing list
> > >
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> > >
> >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > 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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> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Nov 2013 07:26:22 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GPU g_energy problem
> Message-ID:
> <
> CADUqwc6VOTMCw+8F5ioP_c5_qJbo665bGPeyqmYVp5ysJturRQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Nov 25, 2013 at 3:40 AM, Andrei Neamtu <neamtuandrei at gmail.com
> >wrote:
>
> > Dear GMX users,
> >
> > I am simulating a system of two proteins in TIP4P water box. The
> > simulations are performed on a system with 3 servers each containing 16
> CPU
> > cores and 2 Tesla 2090 GPU.
> > The problem thai I encounter is related to the saved interaction energies
> > in the .edr file and read with g_energy.
> >
> > It seems that when using the GPU acceleration none of the interaction
> > energies are saved for the short-range non-bonded interaction computed on
> > the GPU.
> > The SOL (solvent) - SOL LJ-SR and Coul-SR are all ZERO. Also Protein -
> SOL
> > are all zero.
> > When using CPU only accceleration these energies are saved correctly!
> > Despite the zeroes in the energy file the simulations seems to proceed
> > correctly when visually inspected.
> >
> > I wonder in I do not miss something obvious.
> >
> > I am asking if anybody observed a similar behaviour and what should be
> the
> > solution to this problem.
> >
> >
> > I upgraded to 4.6.4 version but also on 4.6.1 the problem was still
> > present.
> >
> >
> Can you clarify if you have re-run the simulation under 4.6.4, not just
> re-analyzed the energies with 4.6.4 g_energy? Doing the latter will have
> no effect if the energies were not saved correctly in the original .edr
> file. http://redmine.gromacs.org/issues/1293 seems relevant here; perhaps
> multiple energygrps still are not supported on GPU.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Nov 2013 07:28:00 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Can't do GB electrostatics; the
> implicit_genborn_params section of the forcefield is missing
> parameters for 9 atomtypes or they might be negative.
> Message-ID:
> <CADUqwc6x8uE=
> w7ee71gc2XtWf4L0CupfSUW3RF1NONt+YKgZ0g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Nov 25, 2013 at 4:53 AM, sunita gupta <sunita.bio at gmail.com>
> wrote:
>
> > Hello everyone,
> >
> > I am trying to do implicit MD of protein-ligand complex using
> > amberff99sb-ildn.
> > I am getting following error at grompp minimization step
> >
> > *GB parameter(s) missing or negative for atom type 'c3'GB parameter(s)
> > missing or negative for atom type 'n2'GB parameter(s) missing or negative
> > for atom type 'ce'GB parameter(s) missing or negative for atom type
> 'os'GB
> > parameter(s) missing or negative for atom type 'cl'GB parameter(s)
> missing
> > or negative for atom type 'h1'GB parameter(s) missing or negative for
> atom
> > type 'hc'GB parameter(s) missing or negative for atom type 'ha'GB
> > parameter(s) missing or negative for atom type
> > 'hn'-------------------------------------------------------Program
> grompp,
> > VERSION 4.5.5Source code file: grompp.c, line: 1123Fatal error:Can't do
> GB
> > electrostatics; the implicit_genborn_params section of the forcefield is
> > missing parameters for 9 atomtypes or they might be negative.For more
> > information and tips for troubleshooting, please check the GROMACSwebsite
> > at http://www.gromacs.org/Documentation/Errors
> > <http://www.gromacs.org/Documentation/Errors>*
> >
> > After reading earlier archive I tried -g disambguate option of acpype,
> but
> > the atomtypes are still case sensitive. Also I tried to modify the
> > gbsa.infile by adding these atomtypes with default vanderwalls radii
> > and chaged
> > two atomtypes in lig.itp by HA and N2 ( which is provided in gbsa.in),
> but
> > the problem is still the same..
> > GB parameter(s) missing or negative for atom type 'HA'
> >
> > GB parameter(s) missing or negative for atom type 'N2'
> >
> > GB parameter(s) missing or negative for atom type 'c3'
> >
> > GB parameter(s) missing or negative for atom type 'ce'
> >
> > GB parameter(s) missing or negative for atom type 'os'
> >
> > GB parameter(s) missing or negative for atom type 'cl'
> >
> > GB parameter(s) missing or negative for atom type 'h1'
> >
> > GB parameter(s) missing or negative for atom type 'hc'
> >
> > GB parameter(s) missing or negative for atom type 'hn'
> >
> > I don't understand why its again complaining about HA and N2, even if it
> is
> > present in lig.itp.
> >
> >
> Their presence in lig.itp is irrelevant; it's the fact that parameters are
> not assigned for these atom types in gbsa.itp in the
> [implicit_genborn_params] directive.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 26 Nov 2013 07:31:07 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
> Mahboobeh Eslami <mahboobeh.eslami at yahoo.com>
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
> <
> CADUqwc4wx+6FP5M2ntE26m6rmpvLd5bP5Cvwk+FtFXk9LDHCFg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Nov 26, 2013 at 4:09 AM, Mahboobeh Eslami <
> mahboobeh.eslami at yahoo.com> wrote:
>
> > hi Dear Gmx Users
> > i want to study the changing of velocity in production stage, do i set
> > gen_vel= yes, gen_temp = 300 and gen_seed = -1 in all mdp file for
> > Equilibration and production or only in production stage? should I
> setother
> > options in the mdp file.
> >
>
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation-
> particularly step 10.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 26 Nov 2013 18:17:04 +0530
> From: sunita gupta <sunita.bio at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Fwd: Can't do GB electrostatics; the
> implicit_genborn_params section of the forcefield is missing
> parameters for 9 atomtypes or they might be negative.
> Message-ID:
> <
> CALgbHJXY9NRwkFbBWZz8eoX3NP02NXEAuwH4ONhbM5ZvMdEFtQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> ---------- Forwarded message ----------
> From: sunita gupta <sunita.bio at gmail.com>
> Date: Mon, Nov 25, 2013 at 3:23 PM
> Subject: Can't do GB electrostatics; the implicit_genborn_params section of
> the forcefield is missing parameters for 9 atomtypes or they might be
> negative.
> To: gmx-users at gromacs.org
>
>
> Hello everyone,
>
> I am trying to do implicit MD of protein-ligand complex using
> amberff99sb-ildn.
> I am getting following error at grompp minimization step
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *GB parameter(s) missing or negative for atom type 'c3' GB parameter(s)
> missing or negative for atom type 'n2'GB parameter(s) missing or negative
> for atom type 'ce'GB parameter(s) missing or negative for atom type 'os'GB
> parameter(s) missing or negative for atom type 'cl' GB parameter(s) missing
> or negative for atom type 'h1'GB parameter(s) missing or negative for atom
> type 'hc'GB parameter(s) missing or negative for atom type 'ha'GB
> parameter(s) missing or negative for atom type 'hn'
> -------------------------------------------------------Program grompp,
> VERSION 4.5.5Source code file: grompp.c, line: 1123Fatal error:Can't do GB
> electrostatics; the implicit_genborn_params section of the forcefield is
> missing parameters for 9 atomtypes or they might be negative. For more
> information and tips for troubleshooting, please check the GROMACSwebsite
> at http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>*
>
> After reading earlier archive I tried -g disambguate option of acpype, but
> the atomtypes are still case sensitive. Also I tried to modify the
> gbsa.infile by adding these atomtypes with default vanderwalls radii
> and chaged
> two atomtypes in lig.itp by HA and N2 ( which is provided in gbsa.in), but
> the problem is still the same..
> GB parameter(s) missing or negative for atom type 'HA'
>
> GB parameter(s) missing or negative for atom type 'N2'
>
> GB parameter(s) missing or negative for atom type 'c3'
>
> GB parameter(s) missing or negative for atom type 'ce'
>
> GB parameter(s) missing or negative for atom type 'os'
>
> GB parameter(s) missing or negative for atom type 'cl'
>
> GB parameter(s) missing or negative for atom type 'h1'
>
> GB parameter(s) missing or negative for atom type 'hc'
>
> GB parameter(s) missing or negative for atom type 'hn'
>
> I don't understand why its again complaining about HA and N2, even if it is
> present in lig.itp.
>
> Kindly guide in tackling this problem.
> Thanks in advance
>
> --
> --
> SUNITA GUPTA
> Senior Research Fellow
> Bioinformatics Centre
> Jawaharlal Nehru University
> New Delhi- 110067
> Email- sunita.bio at gmail.com
>
>
>
>
>
>
> --
> --
> SUNITA GUPTA
> Senior Research Fellow
> Bioinformatics Centre
> Jawaharlal Nehru University
> New Delhi- 110067
> Email- sunita.bio at gmail.com
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
>
>
> End of gromacs.org_gmx-users Digest, Vol 115, Issue 117
> *******************************************************
>
--
--
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio at gmail.com
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