[gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89
Dan Gil
dan.gil9973 at gmail.com
Wed Aug 29 13:45:56 CEST 2018
I think that may indicate that their is something wrong with your input
files, possibly the configuration.
Did you check if the configuration has any bad contacts?
On Wed, Aug 29, 2018 at 7:15 AM sagar bathla <sagarbathla4 at gmail.com> wrote:
> hi Dan,
>
> I got the warnings at the start of the mdrun.
>
> Regards
> Sagar
>
> On Wed, Aug 29, 2018 at 3:30 PM <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> > Today's Topics:
> >
> > 1. free energy of complex system (abhisek Mondal)
> > 2. restrain ligand in free energy. (T?ng Ho?ng)
> > 3. Re: rotation of atoms by more than 90 degrees & LINCS
> > Warnings (Dan Gil)
> > 4. Re: rotation of atoms by more than 90 degrees & LINCS
> > Warnings (Dan Gil)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 29 Aug 2018 11:23:16 +0530
> > From: abhisek Mondal <abhisek.mndl at gmail.com>
> > To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] free energy of complex system
> > Message-ID:
> > <CA+DemH-XhcuMrUQa7yXXbV6E=
> > f3+uLYYkPN2Zi3xg38dCTmRvQ at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> > I'm just trying to calculate free energy of a complex system using
> > following method:
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
> >
> > However, I'm facing some difficulties understanding how can I achieve the
> > goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> > 0.05 spacing for data collection.
> >
> > Now, if I would like to calculate free energy of a complex (say, dimeric
> > protein) then how am I supposed to design the lambda states ?
> > I mean will it be like, one monomer will remain constant and the other
> > monomer goes from lambda=0 to 1 state ? If that be the case then please
> > suggest a way to customize the procedure.
> >
> > Please provide some suggestions.
> > I'm really willing to apply this method in my scenario.
> > Thank you.
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> > *Protein Crystallography Group*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 29 Aug 2018 14:06:31 +0700
> > From: T?ng Ho?ng <hoangtung9597 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] restrain ligand in free energy.
> > Message-ID:
> > <
> > CAFn5Yuf4MYt_Q-XFN5qKdavN25OoUj4SRW-bELE21grnOyKzpQ at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello everyone,
> > i am trying to calculate free energy for complex protein-ligand. but in
> > tutorial it just have methane in water. So i find this
> >
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> > but the problem is i don know how to restrain this ligand.
> > in file complex.top i see that intramolecular - interaction , bond,
> angle ,
> > diheral. and in .mdp file i see bonds_lambda increase. I wonder how i
> can
> > restrain like this . where i can find intramolecular -interaction/....
> > Thank you for your help.
> >
> > Regrads,
> > Tung,
> >
> > --
> > Ho?ng T?ng / student
> > hoangtung9597 at gmail.com / +(84) 0928 478 789
> >
> > University of Medicine and Pharmacy I Ho Chi Minh City
> > 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> > <https://htmlsig.com/signatures/0001DP594H>
> >
> > [image: Facebook] <https://htmlsig.com/t/000001DK2V24> [image: Skype]
> > <https://htmlsig.com/t/000001DH4S28>
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 29 Aug 2018 05:56:14 -0400
> > From: Dan Gil <dan.gil9973 at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> > LINCS Warnings
> > Message-ID:
> > <CAHMQ-OYTxnjHPnLzhU5C6X9YKQ-9aYUzTjqLz5Ksf+U=
> > hoG30Q at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Sagar,
> >
> > At which time step do you get LINCS warnings?
> >
> > Also, please see:
> >
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> >
> > Dan
> >
> > On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbathla4 at gmail.com>
> > wrote:
> >
> > > Dear all,
> > >
> > > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > > triclinic box filled with water. when i am trying to run equillibration
> > > then i am getting too many lincs warnings and simulation has been
> getting
> > > crashed everytime. i have put retraint on all atoms of graphene but
> still
> > > this problem is occuring again.
> > >
> > > My .mdp file looks like this
> > > title = OPLS Graphene IN WATER NVT equilibration
> > > define = -DPOSRES -DFLEXIBLE ; position restrain the protein
> > >
> > > ; Run parameters
> > > integrator = md ; leap-frog integrator
> > > nsteps = 500000 ; 2 * 500000 = 1000 ps
> > >
> > > dt = 0.002 ; 2 fs
> > >
> > > ; Output control
> > > nstxout = 1000 ; save coordinates every 1.0 ps
> > > nstvout = 1000 ; save velocities every 1.0 ps
> > > nstenergy = 1000 ; save energies every 1.0 ps
> > > nstlog = 1000 ; update log file every 1.0 ps
> > >
> > > ; Bond parameters
> > > continuation = yes ; first dynamics run
> > > 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
> > > lincs-warnangle = 90
> > >
> > > ; Neighborsearching
> > > vdw-modifier = Force-switch
> > > cutoff-scheme = Verlet
> > > ns_type = grid ; search neighboring grid cells
> > > nstlist = 10 ; 20 fs, largely irrelevant
> with
> > > Verlet
> > > rcoulomb = 1.2 ; short-range electrostatic
> > cutoff
> > > (in nm)
> > > rvdw = 1.2
> > > rlist = 1.2 ; short-range van der Waals
> > cutoff
> > > (in nm)
> > > rvdw-switch = 1.0
> > > ; 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 = nose-hoover ; nose-hoover thermostat
> > > tc-grps = GRA SOL ; two coupling groups - more accurate
> > > tau_t = 0.1 0.1 ; time constant, in ps
> > > ref_t = 300 300 ; reference temperature, one
> for
> > > each group, in K
> > >
> > > ; Pressure coupling is off
> > > pcoupl = no ; no pressure coupling in NVT
> > >
> > > ; Periodic boundary conditions
> > > pbc = xyz ; 3-D PBC
> > > periodic-molecules = yes
> > >
> > > ; Dispersion correction
> > > DispCorr = EnerPres ; account for cut-off vdW scheme
> > >
> > > ; number of steps for center of mass motion removal =
> > > comm-mode = Linear
> > > nstcomm = 1
> > > comm-grps = GRA SOL
> > > ; Velocity generation
> > > gen_vel = no ; assign velocities from Maxwell
> > > distribution
> > > gen_temp = 300 ; temperature for Maxwell distribution
> > > gen_seed = -1 ; generate a random seed
> > >
> > > ;non equillibrium md
> > > freezegrps: GRA
> > > freezedim: Y Y Y
> > > i have tried various things but nothing is working.
> > > please help to solve this problem
> > >
> > > Regards
> > > Sagar Bathla
> > > --
> > > 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-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Wed, 29 Aug 2018 05:56:14 -0400
> > From: Dan Gil <dan.gil9973 at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> > LINCS Warnings
> > Message-ID:
> > <CAHMQ-OYTxnjHPnLzhU5C6X9YKQ-9aYUzTjqLz5Ksf+U=
> > hoG30Q at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Sagar,
> >
> > At which time step do you get LINCS warnings?
> >
> > Also, please see:
> >
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> >
> > Dan
> >
> > On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbathla4 at gmail.com>
> > wrote:
> >
> > > Dear all,
> > >
> > > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > > triclinic box filled with water. when i am trying to run equillibration
> > > then i am getting too many lincs warnings and simulation has been
> getting
> > > crashed everytime. i have put retraint on all atoms of graphene but
> still
> > > this problem is occuring again.
> > >
> > > My .mdp file looks like this
> > > title = OPLS Graphene IN WATER NVT equilibration
> > > define = -DPOSRES -DFLEXIBLE ; position restrain the protein
> > >
> > > ; Run parameters
> > > integrator = md ; leap-frog integrator
> > > nsteps = 500000 ; 2 * 500000 = 1000 ps
> > >
> > > dt = 0.002 ; 2 fs
> > >
> > > ; Output control
> > > nstxout = 1000 ; save coordinates every 1.0 ps
> > > nstvout = 1000 ; save velocities every 1.0 ps
> > > nstenergy = 1000 ; save energies every 1.0 ps
> > > nstlog = 1000 ; update log file every 1.0 ps
> > >
> > > ; Bond parameters
> > > continuation = yes ; first dynamics run
> > > 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
> > > lincs-warnangle = 90
> > >
> > > ; Neighborsearching
> > > vdw-modifier = Force-switch
> > > cutoff-scheme = Verlet
> > > ns_type = grid ; search neighboring grid cells
> > > nstlist = 10 ; 20 fs, largely irrelevant
> with
> > > Verlet
> > > rcoulomb = 1.2 ; short-range electrostatic
> > cutoff
> > > (in nm)
> > > rvdw = 1.2
> > > rlist = 1.2 ; short-range van der Waals
> > cutoff
> > > (in nm)
> > > rvdw-switch = 1.0
> > > ; 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 = nose-hoover ; nose-hoover thermostat
> > > tc-grps = GRA SOL ; two coupling groups - more accurate
> > > tau_t = 0.1 0.1 ; time constant, in ps
> > > ref_t = 300 300 ; reference temperature, one
> for
> > > each group, in K
> > >
> > > ; Pressure coupling is off
> > > pcoupl = no ; no pressure coupling in NVT
> > >
> > > ; Periodic boundary conditions
> > > pbc = xyz ; 3-D PBC
> > > periodic-molecules = yes
> > >
> > > ; Dispersion correction
> > > DispCorr = EnerPres ; account for cut-off vdW scheme
> > >
> > > ; number of steps for center of mass motion removal =
> > > comm-mode = Linear
> > > nstcomm = 1
> > > comm-grps = GRA SOL
> > > ; Velocity generation
> > > gen_vel = no ; assign velocities from Maxwell
> > > distribution
> > > gen_temp = 300 ; temperature for Maxwell distribution
> > > gen_seed = -1 ; generate a random seed
> > >
> > > ;non equillibrium md
> > > freezegrps: GRA
> > > freezedim: Y Y Y
> > > i have tried various things but nothing is working.
> > > please help to solve this problem
> > >
> > > Regards
> > > Sagar Bathla
> > > --
> > > 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-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > --
> > 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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> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 172, Issue 89
> > ******************************************************
> >
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