[gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 112
Harry Ponce
hponce61 at gmail.com
Wed May 24 00:17:35 CEST 2017
Thank you Mark and Szilárd! I have resorted to freezing the five atoms, and
that has seemed to work, but of course at an energy toll.
- Harrison
On Tue, May 23, 2017 at 3:55 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: (no subject) (Szil?rd P?ll)
> 2. Applying Dihedral Restraints to Polymer in GROMACS 5.1
> (Harry Ponce)
> 3. Re: Using CHARMM36 in GROMACS to simulate polysaccharides
> (Mohammad Hassan Khatami)
> 4. mdrun failure (fatemeh ramezani)
> 5. Re: Applying Dihedral Restraints to Polymer in GROMACS 5.1
> (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 May 2017 16:23:36 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: "Li, Zhixia" <zhixia2 at illinois.edu>
> Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
> <CANnYEw4p4nJ5ODSxoQfkkr9fp+umYyovjcDEx-3=bK0T=CC06g at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Please do not post questions to the list "owner" (=admin) address. Post
> your questions to the users' list instead.
>
> Are you sure you are using the MPI-enabled GROMACS installation? Look in
> the mdrun log header (posting the link to the whole log uploaded to some
> sharing service might also help identifying the issue).
>
> --
> Szil?rd
>
> On Sat, May 20, 2017 at 1:09 AM, Li, Zhixia <zhixia2 at illinois.edu> wrote:
>
> > Hi all,
> >
> > Recently, I want to try hybrid parallelization on two nodes with 12 cores
> > per node. I want it to run 1 mpi per node and 12 openmp per mpi. The
> > command I use is:
> > mpirun -np 2 gmx_mpi mdrun -ntomp 12
> >
> > But I got the output like the following. It seems it only uses one node.
> > Does anyone know how to realize it? And is it the issue of compiling?
> Thank
> > you.
> >
> > Number of logical cores detected (12) does not match the number reported
> > by OpenMP (6).
> > Consider setting the launch configuration manually!
> >
> > Running on 1 node with total 12 cores, 12 logical cores
> > Hardware detected on host taub217 (the node of MPI rank 0):
> > CPU info:
> > Vendor: GenuineIntel
> > Brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
> > SIMD instructions most likely to fit this hardware: SSE4.1
> > SIMD instructions selected at GROMACS compile time: SSE4.1
> >
> > Reading file em4.tpr, VERSION 5.1.4 (single precision)
> > The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 12 (and the command-line setting agreed with that)
> > Using 2 MPI processes
> > Using 12 OpenMP threads per MPI process
> >
> >
> > WARNING: Oversubscribing the available 12 logical CPU cores with 24
> > threads.
> > This will cause considerable performance loss!
> >
> > NOTE: Your choice of number of MPI ranks and amount of resources results
> > in using 12 OpenMP threads per rank, which is most likely inefficient.
> The
> > optimum i$
> >
> >
> > Non-default thread affinity set probably by the OpenMP library,
> > disabling internal thread affinity
> >
> >
> > Best,
> > Zhixia Li
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 23 May 2017 13:48:47 -0400
> From: Harry Ponce <hponce61 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Applying Dihedral Restraints to Polymer in
> GROMACS 5.1
> Message-ID:
> <CAO=3OYzsF2=krHyOUe0BvfNUqg0NqxF2fLaSx21KMZYgq4DtGA at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> I'm attempting to run an energy minimization on some high energy conformers
> of a polymer dimer while restraining two dihedral angles pertaining to the
> five backbone carbons of interest. The literature and forums online are
> sparse when it comes to non-biochemical systems, and it seems as though the
> syntax might have changed over the updated versions of GROMACS.
>
> I've attempted to implement this bit in my topology:
>
> #ifdef DIHRE
>
> [ dihedral_restraints ]
> ; ai aj ak al type label phi dphi kfac power
> 2 1 8 29 1 1 52 0 1 2
> 3 2 1 8 1 1 75 0 1 2
>
> #endif
>
> As well as this bit in my .mdp file:
>
> define = -DDIHRE
> ; Dihedral Restraints
> dihre = yes
> dihre_fc = 1000
> dihre_tau = 0.0
> nstdihreout = 50
>
> I've also tried using what I think is the more recent syntax for applying
> restraints:
>
> ; position restraints for System of UNNAMED
>
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> 2 1 1000 1000 1000
> 3 1 1000 1000 1000
> 8 1 1000 1000 1000
> 29 1 1000 1000 1000
>
> However, when I energy minimize and read the backbone dihedral angles they
> are different than the ones I started with! I am sure I have the correct
> atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them and
> then ignoring my restraints.
>
> Any ideas?
>
> Thank you very much,
> Harrison
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 May 2017 14:16:00 -0400
> From: Mohammad Hassan Khatami <mhk302 at mun.ca>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Using CHARMM36 in GROMACS to simulate
> polysaccharides
> Message-ID: <72BBB4EE-A85C-4694-8DAA-403EBB9D326E at mun.ca>
> Content-Type: text/plain; charset=utf-8
>
> Thank Justin!
> I finished adding the new ?residues? in the .rtp file. pdb2gmx runs
> straight forward. However, while doing energy minimizations, I get several
> errors like the ones below, arise:
>
> ERROR 2 [file topol.top, line 396]:
> No default U-B types
> and
> ERROR 5 [file topol.top, line 550]:
> No default Proper Dih. types
>
> As it says, they might be related to the angles and dihedral parameters.
> Do you have any suggestion on where (and how) to add them?
> Thanks again,
> MH
> >>
> >> On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:
> >>> Hi Justin,
> >>> I am asked to focus on learning how to change and update the CHARMM36
> parameters, so I could implement the future changes and patches easier.
> (Thus, I am not focused in the Glycan Reader, at the moment.)
> >>>
> >>> Thank you! I think I now have a better understanding of what should I
> do. For each part of my polymer,i.e. the initial, the middle and the final
> part, I have to modify the AGLC molecule to represent each of these parts,
> seperately.
> >>> So, lets say to introduce the 1->4 linkage, I need to to apply 14ba
> patch from the top_all36_carb.rtf into the merged.rtp file of GROMACS
> CHARMM36. In this case, I need to create a new version of [ AGLC ] molecule
> (lets call it [ AGLC14 ]) in the merged.rtp, with the changes below from
> the the top_all36_carb.rtf, applied to it:
> >>
> >> Note that your residue name must be limited to 4 characters so it can
> properly be read from the input coordinates. AGLC14 won't work.
> >>
> >>> ! equatorial-axial 1->4 linkage
> >>> PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at
> C4
> >>> dele atom 1HO4
> >>> dele atom 2HO1
> >>> dele atom 2O1
> >>> ATOM 1C4 CC3161 0.09 !
> >>> ATOM 1O4 OC301 -0.36 !
> >>> ATOM 2C1 CC3162 0.29 !
> >>> BOND 1O4 2C1
> >>> I have to remove the HO4, HO1 and O1 lines and modify the values for
> the C4, O4 and C1 atoms. Then, I need to add the bond of
> >>>
> >>> [ bond ]
> >>> ?
> >>> O4 +C1
> >>>
> >>
> >> Correct.
> >>
> >>> Then, I need to apply the bonds and angles parameters in the the
> top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS
> CHARMM36.
> >>> ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL)
> >>> IC 1C3 1C4 1O4 2C1 1.5071 110.40 -86.30 121.00 1.3902 !
> psi
> >>> IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 !
> phi
> >>> IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316
> >>> IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837
> >>>
> >>> I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL)
> values into the merged.vsd file, except for the PHI values. Where (and/or
> how) should I put it?
> >>> Am I on the right track?
> >>
> >> You should not do this. The .vsd file is for defining virtual sites.
> The IC lines are for the CHARMM program's internal coordinate builder,
> specifying some optimized geometry (one that the force field in total
> should produce, or come very close). All the bonded parameters you need
> are already in the force field because they come from the corresponding
> .prm files. Do not adjust bonded parameter files.
> >>
> >> -Justin
> >>
> >>>
> >>> Thanks again for your help.
> >>> MH
> >>>
> >>>
> >>>> On May 19, 2017, at 5:36 PM, Justin Lemkul <jalemkul at vt.edu <mailto:
> jalemkul at vt.edu>> wrote:
> >>>>
> >>>>
> >>>>
> >>>> On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
> >>>>> First, I am looking for 1->4 and 1->6 linkages. In the
> top_all36_carb.rtf file I found different linkages for beta-glucose, but
> non for alpha-glucose.
> >>>>> I am trying to make a simple chain with 1->4 linkages like below:
> >>>>>
> >>>>> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,
> 1->4,alpha-D-glucose.
> >>>>>
> >>>>
> >>>> Linkages are not specific to the sugar; most are totally generic. A
> few comments suggest specific usage and may be corner cases, but your
> patches will be among 14aa, 14ab, 14ba, 14bb.
> >>>>
> >>>>>
> >>>>> Then, I might need to branch them with1->6 linkage.
> >>>>
> >>>> Also totally possible.
> >>>>
> >>>>> I tried Glycan Reader, but itstill crashes.
> >>>>>
> >>>>
> >>>> Uploading a correctly named PDB file should work in Glycan Reader or
> the Quick MD Simulator, but "still crashes" is not diagnostic of anything.
> Specific help with CHARMM-GUI should be brought to their attention, though.
> >>>>
> >>>> -Justin
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 May 2017 18:49:09 +0000 (UTC)
> From: fatemeh ramezani <fr_750 at yahoo.com>
> To: "gmx-users-owner at gromacs.org" <gmx-users-owner at gromacs.org>,
> "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>,
> "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] mdrun failure
> Message-ID: <995000517.513509.1495565349026 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> ?Hi dear gmx-usersI am simulating gold surface- protein interaction by
> GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with
> some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when
> mdrun starts, temperature reaches to 5.50769e+05. md.mdp file containe:
> title??????????? = gold
> cpp?????????? = cpp
> include?????? =
>
> ; RUN CONTROL PARAMETERS
> integrator?????? = md
> comm_mode? = Linear
> ;nstcomm?????? =? 1
> ;comm_grps?? = Protein? Non-protein
> ;nstcalcenergy = 1
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol?????? = 500.0
> emstep??? = 0.001
> tinit????????? = 0.000
> dt???????????? = 0.0005
> nsteps????? = 100000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout???? = 3000
> nstvout???? = 3000
> nstfout????? = 0
> nstlog?????? = 1
> nstenergy???????? = 3000
>
> ; Output frequency and precision for xtc file
> nstxtcout? = 3000
> xtc-precision??? = 3000
>
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> pbc????? = xyz
> periodic_molecules??? = yes
> ; nblist cut-off???????
> rlist?????????????????? = 1.10
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype???? = PME
> r_coulomb??????? = 1.1
> ;pme_order?????? = 6
> ;fourierspacing?? = 0.10
> ewald_rtol??????? = 1e-06
> ewald_geometry????????? = 3d
>
> ; Method for doing Van der Waals
> vdw-type???????????? = switch
> ; cut-off lengths??????
> rvdw-switch?????????? = 0.90
> rvdw???????????????????? = 1.10
>
> ; OPTIONS FOR BONDS???
> constraints?? = none
> constraint-algorithm? =? Lincs
> lincs-order?????????? = 8
> lincs-iter?????????????? = 12
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle???? = 90
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling?
> Tcoupl??????????? = Nose-Hoover
> nhchainlength?? = 1
> ; Groups to couple separately
> tc-grps???????????????? = Protein? SOL NA CL ??? slab AUC
> ; Time constant (ps) and reference temperature (K)
> tau-t??????????????????? =? 0.2 0.2 0.2 0.2 0.2? 0.2
> ref-t???????????????????? =? 300 300 300 300 300 300
>
> ; Non-equilibrium MD stuff
> freezegrps??????????? = slab
> freezedim???????????? = Y Y Y
>
> Can anyone help me to solve this problem?thank you in advance
>
> Fatemeh Ramezani
>
> ------------------------------
>
> Message: 5
> Date: Tue, 23 May 2017 19:55:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Applying Dihedral Restraints to Polymer in
> GROMACS 5.1
> Message-ID:
> <CAMNuMATBF+mp-gbnYD2hAmGmWZ3WnH+7pdVxPMn4scVr7FdW1A at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> It's a restraint - they move in the context of the force field and your
> extra potential. They're not frozen.
>
> Mark
>
> On Tue, May 23, 2017 at 7:49 PM Harry Ponce <hponce61 at gmail.com> wrote:
>
> > Hello,
> >
> > I'm attempting to run an energy minimization on some high energy
> conformers
> > of a polymer dimer while restraining two dihedral angles pertaining to
> the
> > five backbone carbons of interest. The literature and forums online are
> > sparse when it comes to non-biochemical systems, and it seems as though
> the
> > syntax might have changed over the updated versions of GROMACS.
> >
> > I've attempted to implement this bit in my topology:
> >
> > #ifdef DIHRE
> >
> > [ dihedral_restraints ]
> > ; ai aj ak al type label phi dphi kfac power
> > 2 1 8 29 1 1 52 0 1 2
> > 3 2 1 8 1 1 75 0 1 2
> >
> > #endif
> >
> > As well as this bit in my .mdp file:
> >
> > define = -DDIHRE
> > ; Dihedral Restraints
> > dihre = yes
> > dihre_fc = 1000
> > dihre_tau = 0.0
> > nstdihreout = 50
> >
> > I've also tried using what I think is the more recent syntax for applying
> > restraints:
> >
> > ; position restraints for System of UNNAMED
> >
> > [ position_restraints ]
> > ; i funct fcx fcy fcz
> > 1 1 1000 1000 1000
> > 2 1 1000 1000 1000
> > 3 1 1000 1000 1000
> > 8 1 1000 1000 1000
> > 29 1 1000 1000 1000
> >
> > However, when I energy minimize and read the backbone dihedral angles
> they
> > are different than the ones I started with! I am sure I have the correct
> > atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them
> and
> > then ignoring my restraints.
> >
> > Any ideas?
> >
> > Thank you very much,
> > Harrison
> > --
> > Gromacs Users mailing list
> >
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> >
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 157, Issue 112
> *******************************************************
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