[gmx-users] sep and tpo

Mehreen Jan mehreen_jan1990 at yahoo.com
Thu Feb 4 15:16:35 CET 2016






 i just make changes in  gromacs 4.5.5>share>top>gromacs43a1.ff
step of command i performed :
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
>
> from list select the force field
> select 9    which is GROMOS96 43a1 force field
> select the water model:
> 1    SPC simple point charge
> then error message
> fatal error:
> residue SEP /TPO not found in residue topology database






















--------------------------------------------
On Thu, 4/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

 Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 24
 To: gromacs.org_gmx-users at maillist.sys.kth.se
 Received: Thursday, 4 February, 2016, 5:53 PM
 
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 Today's Topics:
 
    1. Wall potential different results for
 12-6 and table
       (Sudharsan Pandiyan)
    2. Re: Fwd: FW: PME settings in free
 energy calculations
       (Dries Van Rompaey)
    3. Re: C_v and Temperature (Alexander
 Alexander)
    4. Re: trjconv options? (Justin Lemkul)
    5. Re: $GMXLIB or the working directory
 (Justin Lemkul)
 
 
 ----------------------------------------------------------------------
 
 Message: 1
 Date: Thu, 4 Feb 2016 11:34:43 +0000
 From: Sudharsan Pandiyan <sudharsan.pandiyan at chem.kuleuven.be>
 To: "gmx-users at gromacs.org"
 <gmx-users at gromacs.org>
 Subject: [gmx-users] Wall potential different results for
 12-6 and
     table
 Message-ID:
     <4A1AE85DA03CB144A9DE9FCDD245E17D218FC763 at ICTS-S-MBX7.luna.kuleuven.be>
     
 Content-Type: text/plain; charset="iso-8859-1"
 
 Dear Gmx users,
 
 I am trying to simulate a wall potential using tabulated
 potentials option. But it gives different potential values
 when compared to the 12-6 option when I use same sigma and
 epsilon values that are used to build the table. I intend to
 modify my table potential later to more detailed form so I
 have to make sure that it produces correct result. But my
 check seems to show that there is a difference between using
 12-6 and tabulated potentials for wall interaction. Could
 any one of you what is the difference and how can I get the
 correct potential for tabulated form?
 
 PS: In the manual, its written that both 9-3 and 10-4 are
 integrated over the surface area and 12-6 potential was
 applied directly with the z-distance. But how the tabulated
 potential is represented? (section 7.3.20)
 
 Sincerely,
 
 Sudharsan
 
 
 
 
 ------------------------------
 
 Message: 2
 Date: Thu, 4 Feb 2016 12:59:34 +0100
 From: Dries Van Rompaey <dries.vanrompaey at gmail.com>
 To: gromacs.org_gmx-users at maillist.sys.kth.se
 Subject: Re: [gmx-users] Fwd: FW: PME settings in free
 energy
     calculations
 Message-ID:
    
 <CAJefogcLAspn_6PHRiYdimcxXEDo4saQE2BQLFarcAmqopci+g at mail.gmail.com>
 Content-Type: text/plain; charset=UTF-8
 
 Hi,
 
 I'm using PME with the default Potential-Shift-Verlet
 modifier. If I'm
 interpreting the manual and comments on the mailinglist
 correctly, the
 settings for rcoulomb-switch shouldn't affect this and
 PME-switching
 shouldn't be necessary (although there seems to have been
 some discussion
 about this, https://gerrit.gromacs.org/#/c/2220/).
 Has a consensus been
 reached elsewhere?
 
 Current nonbonded settings in my .mdp files are:
 ; Electrostatics
 coulombtype             
 = PME
 rcoulomb             
       = 1.0
 
 ; van der Waals
 vdwtype             
       = cutoff
 vdw-modifier            =
 Potential-switch
 rvdw-switch             
 = 0.9
 rvdw               
          = 1.0
 
 ; Apply long range dispersion corrections for Energy and
 Pressure
 DispCorr             
     = EnerPres
 
 ; Spacing for the PME/PPPM FFT grid
 fourierspacing       
    = 0.08
 
 ; EWALD/PME/PPPM parameters
 pme_order             
   = 6
 ewald_rtol             
    = 1e-06
 epsilon_surface        = 0
 
 Thanks in advance,
 
 Dries
 
 On 4 February 2016 at 00:56, Michael Shirts <mrshirts at gmail.com>
 wrote:
 
 > Hi, Dries-
 >
 > Questions like this are probably best answered on the
 gmx-users list.
 > I can't say too much for the Verlet scheme -- I know
 that it was
 > relatively recently adapted for free energies, and
 there may be some
 > combinations of settings that could give unanticipated
 results.
 >
 > Pretty much all of our experience about nonbonded
 calculations and
 > free energies is collected in the following paper:
 > http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used
 the group
 > cutoff scheme since that was the only one that was
 supported in
 > GROMACS at the time.
 >
 > Since you haven't sent any files, it's hard to tell
 what is actually
 > going on. The one thing that has a tendency to happen
 with the more
 > recent update schemes is if you set a potential
 modifier that is a
 > switch, but don't set the distance the switch starts
 at, then it is
 > automatically set to zero.  Check the mdout.mdp to
 see if this is
 > happening.
 >
 > > From: Van Rompaey Dries <Dries.VanRompaey at uantwerpen.be>
 > Date: Wednesday, February 3, 2016 at 12:34 PM
 > To: Michael Shirts <michael.shirts at colorado.edu>
 > Subject: PME settings in free energy calculations
 >
 > Dear prof. Shirts,
 >
 > I'm currently trying to figure out the PME settings for
 a relative
 > free binding energy simulation I'm working on. I took
 the parameters
 > from Matteo Aldeghi's
 > paper(
 > http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract
 > )
 > as a starting point (adapted for the Verlet scheme by
 scaling the
 > fourierspacing to 0.08 and setting coulomb = rvdw =
 1.0). I then tried
 > to verify these settings by comparing a single point
 energy
 > calculation with these settings and one with very long
 coulomb cutoffs
 > as recommended on alchemistry.org.
 >
 > Unfortunately, I can't seem to get this quite right.
 I'm getting
 > differences in the hundreds of kj/mol, leading me to
 suspect I'm doing
 > something wrong. I'm calculating the energy values by
 extracting
 > CoulombSR and Coul-recip from the energy.xvg files.
 I've tried
 > calculating the energy with coulomb cutoffs at 3 nm and
 10 nm, but
 > agreement with the PME results remains rather poor.
 David Mobley
 > mentioned you performed extensive research on this
 topic, and I'm
 > hoping you could point me in the right direction.
 >
 > Thanks in advance,
 >
 > Dries
 >
 >
 >
 > ~~~~~~~~~~~~~~~~
 > Michael Shirts
 > Associate Professor
 > michael.shirts at colorado.edu
 > Phone: (303) 735-7860
 > Office: JSCBB D317
 > Department of Chemical and Biological Engineering
 > University of Colorado Boulder
 > --
 > 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: 3
 Date: Thu, 4 Feb 2016 13:27:36 +0100
 From: Alexander Alexander <alexanderwien2k at gmail.com>
 To: gmx-users at gromacs.org
 Subject: Re: [gmx-users] C_v and Temperature
 Message-ID:
     <CAEDv6u6oBgrFs7RHVHWkcSiS9D6xL-9FZ376uWSKOBp0KkXn_A at mail.gmail.com>
 Content-Type: text/plain; charset=UTF-8
 
 Thank you for your response.
 
 I am trying to calculate the heat capacity at constant
 volume for a crystal
 solid in different temperature; below are what "gmx energy
 -fluct_props
 ..." gives me in 4 different temperatures:
 
 T = 29.9    Cv = 24.4681 J/mol K
 
 T = 99.9    Cv = 24.6643 J/mol K
 
 T = 297.9  Cv = 24.4926 J/mol K
 
 T = 799.9  Cv = 24.5054 J/mol K
 
 And "gmx dos" gives something around "Heat capacity
 0.000683396 (J/mol K)"
 as quantum correction for all the simulation temperature I
 have tried.
 
 The result for the two last temperature is fascinating and
 agree well with
 my DFPT and phonon calculations as well as all the heat
 capacity laws in
 higher temperatures.
 Also, I was expecting that the C_v reduces to around 2 or 3
 J/mol K  in
 lower temperatures, but I do not know why the C_v in lower
 temperature is
 the same as higher temperature, although I had a well
 prepared and
 converged calculations. So, I would be so thankful if one
 could comment on
 this.
 
 By the way, this is what I have in my dos.log file.
 ----------------------------
 System = "A3B crystal Solid"
 Nmol = 43904
 Natom = 43904
 dt = 0.2 ps
 tmass = 2.05132e+06 amu
 V = 415.228 nm^3
 rho = 8203.43 g/l
 T = 298.15 K
 beta = 0.403395 mol/kJ
 
 DoS parameters
 Delta = 3.49303e-05
 fluidicity = 0.00202656
 hard sphere packing fraction = 441.911
 hard sphere compressibility = 1.00454
 ideal gas entropy = 0.0717008
 hard sphere entropy = -0.762789
 sigma_HS = 1.99851 nm
 DoS0 = 2.3222
 Dos2 = 627309
 DoSTot = 6.19421
 Diffusion coefficient from VACF 0.000169117 10^-5 cm^2/s
 Diffusion coefficient from DoS 0.00023386 10^-5 cm^2/s
 Heat capacity 0.000623269 J/mol K
 ------------------------------------------
 
 Best regards,
 Alex
 
 
 
 On Thu, Feb 4, 2016 at 8:45 AM, David van der Spoel <spoel at xray.bmc.uu.se>
 wrote:
 
 > On 03/02/16 23:52, Alexander Alexander wrote:
 >
 >> Dear Gromacs user,
 >>
 >> Normally there is a "*ref-t" [K]  *in .mdp
 file as reference temperature
 >> in
 >> NVT calculation, in addition, yet another
 Temperature must be indicated in
 >> "gmx dos *-T* XXX ..." for example in heat capacity
 (C_v) calculation with
 >> quantum correction. So, I was wondering that which
 of these two
 >> temperatures is the one that the heat capacity
 (C_v) has been calculated
 >> in
 >> to be reported later?
 >>
 > To get the simulation temperature run gmx energy
 >
 >
 >> One more question:
 >> In C_v calculation, would you please confirm me
 that the "gmx dos" would
 >> give only the quantum correction for C_v? Not the
 total C_v including
 >> quantum correction.
 >> IF so, then, the Total C_v  would be:
 >> Total C_v = "gmx energy -nmol -fluct_props" + "gmx
 dos -T ..."
 >>
 > Have you checked the output from gxm dos?
 > It describes everything in quite some detail.
 >
 >
 >> Thank you so much.
 >>
 >> Cheers,
 >>
 >> Alex
 >>
 >>
 >
 > --
 > David van der Spoel, Ph.D., Professor of Biology
 > Dept. of Cell & Molec. Biol., Uppsala University.
 > Box 596, 75124 Uppsala, Sweden. Phone: 
 +46184714205.
 > spoel at xray.bmc.uu.se 
   http://folding.bmc.uu.se
 > --
 > 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: Thu, 4 Feb 2016 07:51:27 -0500
 From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org
 Subject: Re: [gmx-users] trjconv options?
 Message-ID: <56B3494F.4070703 at vt.edu>
 Content-Type: text/plain; charset=windows-1252;
 format=flowed
 
 
 
 On 2/4/16 4:27 AM, Timofey Tyugashev wrote:
 >
 >
 >> Message: 2
 >> Date: Wed, 3 Feb 2016 07:37:42 -0500
 >> From: Justin Lemkul<jalemkul at vt.edu>
 >> To:gmx-users at gromacs.org
 >> Subject: Re: [gmx-users] trjconv options?
 >> Message-ID:<56B1F496.5090604 at vt.edu>
 >> Content-Type: text/plain; charset=windows-1252;
 format=flowed
 >>
 >>
 >>
 >> On 2/3/16 6:34 AM, Timofey Tyugashev wrote:
 >>> >Thank you for replies on my previous
 questions.
 >>> >And now I have another one dealing with
 trjconv.
 >>> >
 >>> >I have a simulation of  a three-chain
 protein/nucleic acid complex. Naturally,
 >>> >it gets broken in three separate strands by
 PBC.
 >>> >After trying several, I settled on using
 options '-pbc mol' with '-ur compact'
 >>> >which makes the complex look decent again
 and it looks like that does the job.
 >>> >But I'm worried about a possibility of
 something getting unrepaired by this
 >>> >option and getting unnoticed by me. What is
 the way to check for it?
 >> Any molecules that appear to fly away suddenly will
 be a pretty dead giveaway.
 >>
 >> In general, for multimeric complexes, you need to
 do a lot more work, e.g.
 >> centering on a single chain after making molecules
 whole and removing jumps.  If
 >> a simple -pbc mol -ur compact does the trick,
 probably nothing has actually
 >> crossed a periodic boundary yet.
 >>
 >>> >Also it keeps tumbling around the cell
 during the trajectory. It's annoying. Is
 >>> >there a way to pin down the cluster and
 stop it from rotating?
 >> This is what trjconv -fit is for.
 >>
 >> -Justin
 > Well, both vmd and pymol render .gro file (and
 trajectory files) with DNA
 > strands and protein positioned in different corners of
 the box.
 > Also, editconf -pbc has no effect on .gro file with the
 broken complex. How it's
 > supposed to behave?
 >
 > So in this case I should at first run trjconv with
 '-pbc whole', make second run
 > with '-pbc nojump', then make third run with '-pbc mol'
 to properly repair the
 > trajectory?
 > I guess for -fit I should pick 'progressive' option?
 
 Complex systems require complex operations.  Start with
 
 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
 
 because that order of operations generally works well. 
 Then see posts in the 
 archive, because this comes up frequently.  Typically,
 after making molecules 
 whole and removing jumps, you can center on a custom index
 group that defines 
 some useful center.  Then you can do whatever fitting
 you like.
 
 -Justin
 
 -- 
 ==================================================
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalemkul at outerbanks.umaryland.edu
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==================================================
 
 
 ------------------------------
 
 Message: 5
 Date: Thu, 4 Feb 2016 07:53:06 -0500
 From: Justin Lemkul <jalemkul at vt.edu>
 To: Mehreen Jan <mehreen_jan1990 at yahoo.com>
 Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
 Subject: Re: [gmx-users] $GMXLIB or the working directory
 Message-ID: <56B349B2.80808 at vt.edu>
 Content-Type: text/plain; charset=utf-8; format=flowed
 
 
 Please continue this discussion on the gmx-users mailing
 list.  I am not a 
 private help service.
 
 On 2/4/16 12:13 AM, Mehreen Jan wrote:
 > respected sir!
 > thank so much for reply and time
 > respected sir i have no idea about  whic kind of
 changes are required for $GMXLIB or the working directory
 >
 > i just make changes in  gromacs
 4.5.5>share>top>gromacs43a1.ff . i have done no
 changes in $GMXLIB and i dont know what type of changes are
 / i required for $GMXLIB.
 > snapshots are attached of all steps kindly find the
 attachment.
 >
 > step of command i performed :
 > pdb2gmx -f protein.pdb -p protein.top -o protein.gro
 >
 > from list select the force field
 > select 9    which is GROMOS96 32a1 force
 field
 > select the water model:
 > 1    SPC simple point charge
 > then error message
 > fatal error:
 > residue SEP /TPO not found in residue topology
 database
 >
 
 Stop trying to modify 43A1; you likely aren't familiar
 enough with the structure 
 and file formats.
 
 Use the 43A1p files directly.  They work.  I
 verified it yesterday.  Download 
 the force field archive, put it in your working directory or
 GMXLIB and use it. 
   Don't use 43A1 because it simply won't work. 
 This much should be clear based 
 on the repetition of the exact same error message every time
 you do anything.
 
 -Justin
 
 -- 
 ==================================================
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalemkul at outerbanks.umaryland.edu
 | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==================================================
 
 
 ------------------------------
 
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