[gmx-users] gmx-users Digest, Vol 98, Issue 42
PAVAN PAYGHAN
pavanapex at gmail.com
Thu Jun 7 14:51:06 CEST 2012
Dear Mark,
Thank you very much for the reply.
To clarify , I have asked all the warning based questions to get
acknowledged with your expert opinion, apart from the manual based view.
According to your suggestion NPT with Position restraints is messy,but
still I have seen lots of manual/tutorial (including Bevans Lab )
suggesting the position restraining of protein during NVT as well as NPT.
That is the reason I have followed the same. Please clarify your view on
this matter.
Thak you very much in advance.
Pavan Payghan
On Thu, Jun 7, 2012 at 4:58 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Warnings related to Berendsen pressure coupling and use
> the refcoord_scaling option (Mark Abraham)
> 2. Re: GPU crashes (Justin A. Lemkul)
> 3. Re: Re: change in rename of 1POPC to 1LIG though coordinate
> and atom same in 1LIG of 1POPC, during solvation of system
> (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 07 Jun 2012 20:42:47 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Warnings related to Berendsen pressure
> coupling and use the refcoord_scaling option
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FD085A7.5000403 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote:
> >
> >
> > Dear Gromacs Users,
> >
> > I am using gromacs version 4.5.5.and running my jobs on single
> > node with 8 cores. My system contains about 425000 atoms (protein +
> > Lipid +SOL). I have successfully reached up to Energy minimization
> > step.As per the suggestion by Dear Mark, I am starting my NPT
> > equilibration with Berendsen and further with Parinello-Rahman to get
> > the right ensemble.But when I am trying for NPT equilibration with
> > Berendsen, getting following Warnings.
> >
> > WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling
> > invalidates the true ensemble for the thermostat
> >
> > WARNING 2 [file npt.mdp]: You are using pressure coupling with
> > absolute position restraints, this will give artifacts. Use the
> > refcoord_scaling option.
> >
> > And about 10 such LINCS warnings while running the job as shown below:
> >
> > Step 39, time 0.078 (ps)LINCS WARNING
> >
> > relative constraint deviation after LINCS:
> >
> > rms 0.000029, max 0.000473 (between atoms 890 and 891)
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> > 12050 12049 31.2 0.1000 0.1000 0.1000
> > 11721 11720 46.0 0.1000 0.1000 0.1000
> > 5496 5495 36.8 0.1000 0.1000 0.1000
> >
> > With --maxwarn option I am able to run it, and output density and
> > pressure seems perfectly alright.
> >
> > Based on the same I want to know:-
> >
> > 1. How does pressure coupling with Berendsen invalidates the true
> > ensemble?
> >
>
> See manual sections for T and P coupling for introductory discussion.
>
> > At least for initial fixing of density and pressure?
> >
> > Whether to bother for above mentioned warning or ignore it?
> >
>
> Since you're going to do more equilibration after this, you be the judge.
>
> > 2. Pressure coupling with absolute position restraints warning how it
> > will lead to artifacts?
> >
> > How one can use refcoord_scaling option in this situation?
> >
>
> See manual.
>
> > Whether to bother for above mentioned warning or ignore it?
> >
>
> Position restraints and NPT is messy. Choose your poison.
>
> > 3. Using Berendsen with semiisotropic couple type is wrong method or
> > no such problem?
> >
> > Please suggest me whether to move ahead with ignorance to the warnings
> > or to change some parameters in mdp file?
> >
>
> That's your judgement to make. How does your preparation protocol
> compare to the ones you have read about in the recent literature?
>
> Mark
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>
> Message: 2
> Date: Thu, 07 Jun 2012 07:25:31 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] GPU crashes
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FD08FAB.5000004 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
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>
>
> On 6/7/12 3:57 AM, lloyd riggs wrote:
> > Did you play with the time step? Just currious, but I woundered what
> > happened with 0.0008, 0.0005, 0.0002. I found if I had a good behaving
> > protein, as soon as I added a small (non-protein) molecule which rotated
> > wildly while attached to the protein, it would crash unless I reduced the
> > time step to the above when constraints were removed after EQ ... always
> it
> > seemed to me it didnt like the rotation or bond angles, seeing them as a
> > violation but acted like it was an amino acid? (the same bond type but
> with
> > wider rotation as one end wasnt fixed to a chain) If your loop moves via
> > backbone, the calculated angles, bonds or whatever might appear to the
> > computer to be violating the parameter settings for problems, errors,
> etc as
> > it cant track them fast enough over the time step. Ie atom 1-2-3 and then
> > delta 1-2-3 with xyz parameters, but then the particular set has
> additional
> > rotation, etc and may include the chain atoms which bend wildly
> (n-Ca-Cb-Cg
> > maybe a dihedral) but proba! bly not this.
> >
> > Just a thought but probably not the right answere as well, it might be
> the
> > way it is broken down (above) over GPUs, which convert everything to
> > matricies (non-standard just for basic math operations not real
> matricies per
> > say) for exicution and then some library problem which would not account
> for
> > long range rapid (0.0005) movements at the chain (Ca,N,O to something
> else)
> > and then tries to apply these to Cb-Cg-O-H, etc using the initial points
> > while looking at the parameters for say a single amino acid...Maybe the
> > constraints would cause this, which would make it a pain to EQ, but this
> > allowed me to increase the time step, but would ruin the experiment I had
> > worked on as I needed it unconstrained to show it didnt float away when
> > proteins were pulled, etc...I was using a different integrator
> though...just
> > normal MD.
> >
>
> I have long wondered if constraints were properly handled by the OpenMM
> library.
> I am constraining all bonds, so in principle, dt of 0.002 should not be a
> problem. The note printed indicates that the constraint algorithm is
> changed
> from the one selected (LINCS) to whatever OpenMM uses (SHAKE and a few
> others in
> combination). Perhaps I can try running without constraints and a reduced
> dt,
> but I'd like to avoid it.
>
> I wish I could efficiently test to see if this behavior was GPU-specific,
> but
> unfortunately the non-GPU implementation of the implicit code can
> currently only
> be run in serial or on 2 CPU due to an existing bug. I can certainly test
> it,
> but due to the large number of atoms, it will take several days to even
> approach
> 1 ns.
>
> > ANd your cutoffs for vdw, etc...Why are they 0? I dont know if this
> means a
> > defautl set is then used...but if not ? Wouldnt they try integrating
> using
> > both types of formula, or would it be just using coulumb or vice versa?
> (dont
> > know what that would do to the code but assume it means no vdw, and all
> > coulumb but then zeros are alwyas a problem for computers).
> >
>
> The setup is for the all-vs-all kernels. Setting cutoffs equal to zero and
> using a fixed neighbor list triggers these special optimized kernels. I
> have
> also noticed that long, finite cutoffs (on the order of 4.0 nm) lead to
> unacceptable energy drift and structural instability in well-behaved
> systems
> (even the benchmarks). For instance, the backbone RMSD of lysozyme is
> twice as
> large in the case of a 4.0-nm cutoff relative to the all-vs-all setup, and
> the
> energy drift is quite substantial.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 07 Jun 2012 07:27:54 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though
> coordinate and atom same in 1LIG of 1POPC, during solvation of
> system
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FD0903A.5080603 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 6/6/12 1:12 PM, Sangita Kachhap wrote:
> >
> >> Send gmx-users mailing list submissions to
> >> gmx-users at gromacs.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> or, via email, send a message with subject or body 'help' to
> >> gmx-users-request at gromacs.org
> >>
> >> You can reach the person managing the list at
> >> gmx-users-owner at gromacs.org
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of gmx-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: Re: change in rename of 1POPC to 1LIG though coordinate
> >> and atom same in 1LIG of 1POPC, during solvation of system
> >> (Justin A. Lemkul)
> >> 2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann)
> >> 3. energy conservation: shift vs shifted user potential
> >> (Anja Kuhnhold)
> >> 4. Cannot get correct pressure value with MTTK pressure coupling
> >> (Bao Kai)
> >> 5. Re: Cannot get correct pressure value with MTTK pressure
> >> coupling (Justin A. Lemkul)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Wed, 06 Jun 2012 08:56:04 -0400
> >> From: "Justin A. Lemkul"<jalemkul at vt.edu>
> >> Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though
> >> coordinate and atom same in 1LIG of 1POPC, during solvation of
> system
> >> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> >> Message-ID:<4FCF5364.800 at vt.edu>
> >> Content-Type: text/plain; charset=UTF-8; format=flowed
> >>
> >>
> >>
> >> On 6/6/12 8:52 AM, Sangita Kachhap wrote:
> >>
> >>>> On 6/6/12 3:09 AM, Sangita Kachhap wrote:
> >>>>>
> >>>>> Hello all
> >>>>> I have to do MD simulation of membrane protein having docked ligand
> in POPC
> >>>>> lipid bilayer.
> >>>>> I am geeting error during solvation of system:
> >>>>> Resname of 1POPC in system_shrink1.gro converted into 1LIG
> >>>>>
> >>>>>
> >>>>> I have done following:
> >>>>>
> >>>>> GROMACS COMMAND
> >>>>>
> >>>>> 1) Generate topol.top using GROMOS96 53A6 parameter set
> >>>>> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc
> >>>>>
> >>>>>
> >>>>> at prompt select 14
> >>>>>
> >>>>> 2) Download:
> >>>>> * popc128.pdb - the structure of a 128-lipid POPC bilayer
> >>>>> * popc.itp - the moleculetype definition for POPC
> >>>>> * lipid.itp - Berger lipid parameters
> >>>>>
> >>>>> from
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
> >>>>>
> >>>>> 3) Modify topol.top with:
> >>>>> #include "gromos53a6.ff/forcefield.itp"
> >>>>>
> >>>>> to:
> >>>>>
> >>>>> #include "gromos53a6_lipid.ff/forcefield.itp"
> >>>>>
> >>>>>
> >>>>> &
> >>>>>
> >>>>> ; Include Position restraint file
> >>>>> #ifdef POSRES
> >>>>> #include "posre.itp"
> >>>>> #endif
> >>>>> ; Include ligand topology
> >>>>> #include "ligand-full.itp"
> >>>>>
> >>>>> ; Include POPC chain topology
> >>>>> #include "popc.itp"
> >>>>>
> >>>>> ; Include water topology
> >>>>> #include "gromos53a6_lipid.ff/spc.itp"
> >>>>>
> >>>>> and at the end add LIG 1 in [molecules]
> >>>>>
> >>>>> 4) cp files
> >>>>> aminoacids.rtp
> >>>>> aminoacids.hdb
> >>>>> aminoacids.c.tdb
> >>>>> aminoacids.n.tdb
> >>>>> aminoacids.r2b
> >>>>> aminoacids.vsd
> >>>>> ff_dum.itp
> >>>>> ffnonbonded.itp
> >>>>> ffbonded.itp
> >>>>> forcefield.itp
> >>>>> ions.itp
> >>>>> spc.itp
> >>>>> watermodels.dat
> >>>>>
> >>>>> from gromacs top to directory named gromos53a6_lipid.ff in working
> >>>>> directory.
> >>>>> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes
> ])from
> >>>>> lipid.itp to ffnonbonded.itp& ffbonded.itp and create a
> forcefield.doc
> >>>>> file
> >>>>> that contains a description of the force field parameters contain
> "GROMOS96
> >>>>> 53A6
> >>>>> force field, extended to include Berger lipid parameters".
> >>>>> Delete line ";; parameters for lipid-GROMOS interactions." and its
> >>>>> subsequent
> >>>>> line, change HW as H of [ nonbond_params ]
> >>>>>
> >>>>>
> >>>>> 5) Generate .tpr for POPC
> >>>>> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr
> -maxwarn 1
> >>>>> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
> >>>>>
> >>>>>
> >>>>> 6) Remove periodicity
> >>>>> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur
> compact
> >>>>> (at command prompt select 0)
> >>>>>
> >>>>>
> >>>>> 7) Oriant the protein within the same coordinate as written in end of
> >>>>> popc128a_whole.gro
> >>>>> editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro
> -c -box
> >>>>> 6.23910 6.17970 6.91950
> >>>>>
> >>>>>
> >>>>> 8) Pack lipid around protein
> >>>>> cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro> system.gro
> >>>>>
> >>>>> Remove unnecessary lines (the box vectors from the KALP structure,
> the
> >>>>> header
> >>>>> information from the DPPC structure and update the second line of the
> >>>>> coordinate file (total number of atoms) accordingly.
> >>>>>
> >>>>> 9) Modify topol.top to add positional restrain on protein
> >>>>>
> >>>>> ; Include Position restraint file
> >>>>> #ifdef POSRES
> >>>>> #include "posre.itp"
> >>>>> #endif
> >>>>>
> >>>>> ; Strong position restraints for InflateGRO
> >>>>> #ifdef STRONG_POSRES
> >>>>> #include "strong_posre.itp"
> >>>>> #endif
> >>>>>
> >>>>> ; Include DPPC chain topology
> >>>>> #include "dppc.itp"
> >>>>>
> >>>>> ; Include water topology
> >>>>> #include "gromos53a6_lipid.ff/spc.itp"
> >>>>>
> >>>>> &
> >>>>> Genrate new positional restraint
> >>>>> genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc
> 100000
> >>>>> 100000
> >>>>> 100000
> >>>>> for system (protein + ligand)
> >>>>> Add a line "define = -DSTRONG_POSRES" to .mdp file
> >>>>>
> >>>>>
> >>>>> 10) addion POPC 128 to topol.top
> >>>>>
> >>>>>
> >>>>> 11) Scale down lipid
> >>>>> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5
> >>>>> area_shrink1.dat
> >>>>>
> >>>>>
> >>>>>
> >>>>> 12) Solvate with water
> >>>>>
> >>>>> Copy vdwradii.dat from Gromacs top to working directory and change
> the value
> >>>>> of
> >>>>> C from 0.15 to 0.375(to avoid addition of water in lipid
> hydrohphobic core)
> >>>>>
> >>>>> genbox -cp system_shrink1.gro -cs spc216.gro -o
> system_shrink1_solv.gro -p
> >>>>> topol.top
> >>>>>
> >>>>>
> >>>>> Upto 11th step .gro file is OK conatin protein resid 32-254, ligand
> 1LIG,
> >>>>> POPC
> >>>>> resid 1-128 and solvent
> >>>>>
> >>>>> After 12th step in gro file protein is there 32-254, Ligand 1LIG but
> POPC
> >>>>> resid
> >>>>> 2-128 because resid 1 of POPC is converted to 1LIG though all
> cordinate and
> >>>>> atom
> >>>>> name are same of 1POPC in 1LIG.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Anybody please suggest me why this change in rename is occuring.
> >>>>>
> >>>>
> >>>> Based on the description, you say in step (3) that you add "LIG 1" to
> the end
> >>>> of
> >>>> [molecules], but then in (12) you give the order as protein, ligand,
> then
> >>>> POPC.
> >>>> The order of the coordinate file and [molecules] must match,
> otherwise
> >>>> funny
> >>>> things happen. If you have protein, ligand, and POPC, you must list
> the
> >>>> moleculetype names in that order in [molecules].
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Thanks for reply
> >>> In step 3 I added "LIG 1" to the end of [molecules] because when I
> used
> >>> command "pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc"
> to
> >>> generate topol.top it already contain "Protein_chain_A 1" in
> [molecules] so I
> >>> added only "LIG 1"
> >>>
> >>>
> >>> This is end of topol.top after solvation
> >>>
> >>> [ molecules ]
> >>> ; Compound #mols
> >>> Protein_chain_A 1
> >>> LIG 1
> >>> POPC 128
> >>> SOL 1829
> >>>
> >>>
> >>>
> >>
> >> OK, that makes sense. Did InflateGRO remove any lipids? If it did,
> that is not
> >> reflected correctly in the topology.
> >
> >
> >
> >
> > No it did,nt. After using InflaterGRO it tells 64 lipid in uper leaflet
> and 64
> > in lower leaflet so there are total 128 lipid before and after scaling
> down.
> >
>
> That's bizarre. Even the smallest protein should cause some lipid overlap,
> unless your initial scaling factor was enormous. Also note that
> InflateGRO will
> indeed report that there are 64 lipids per leaflet, but only later in the
> screen
> output will it state whether or not it is removing any lipids.
>
> The only feasible source of error I can think of is that there is a
> mismatch
> between the coordinate and topology files, but given the information at
> hand I
> can't see its origin. Check all your steps again carefully, verify the
> contents
> of the coordinate file using external means (counting via grep, etc), and
> if all
> else fails, start again, making sure of each step along the way.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
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> End of gmx-users Digest, Vol 98, Issue 42
> *****************************************
>
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