[gmx-users] Re : gromacs.org_gmx-users Digest, Vol 152, Issue 55

Adel ASCHI aschi13 at yahoo.fr
Sat Dec 17 09:26:31 CET 2016


Dear Sir,
I want to use the gromacs server, but, the probleme,how i can obtain the Certificate Authority. by the way i'm from tunisia 
can you help me for this
Yours Sincerely

PhD. ASCHI Adel 
Lab. de Physique de la Matière Molle 
Département de Physique 
Faculté des Sciences de Tunis; Campus Universitaire. 1060. Tunisia 
Phone: 216 71 872 600  Phax : 216 71 885 073 
e-mail: aschi13 at yahoo.fr

--------------------------------------------
En date de : Ven 16.12.16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> a écrit :

 Objet: gromacs.org_gmx-users Digest, Vol 152, Issue 55
 À: gromacs.org_gmx-users at maillist.sys.kth.se
 Date: Vendredi 16 décembre 2016, 22h26
 
 Send gromacs.org_gmx-users mailing
 list submissions to
     gromacs.org_gmx-users at maillist.sys.kth.se
 
 To subscribe or unsubscribe via the World Wide Web, visit
     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or, via email, send a message with subject or body 'help'
 to
     gromacs.org_gmx-users-request at maillist.sys.kth.se
 
 You can reach the person managing the list at
     gromacs.org_gmx-users-owner at maillist.sys.kth.se
 
 When replying, please edit your Subject line so it is more
 specific
 than "Re: Contents of gromacs.org_gmx-users digest..."
 
 
 Today's Topics:
 
    1. Manual refinement of ATB topologies ?
 (Sim gmx)
    2. Re: CG Lincs errors (Nash, Anthony)
    3. Re: Desolvation or hydration free
 energy of an ION (Justin Lemkul)
 
 
 ----------------------------------------------------------------------
 
 Message: 1
 Date: Fri, 16 Dec 2016 13:46:43 +0100
 From: Sim gmx <simgmx at gmail.com>
 To: gromacs.org_gmx-users at maillist.sys.kth.se
 Subject: [gmx-users] Manual refinement of ATB topologies ?
 Message-ID:
     <CAFNohVmw7QTj5g5sMBcugZuxcO7Z_hA4dbZA_8reNwgjngo29g at mail.gmail.com>
 Content-Type: text/plain; charset=UTF-8
 
 Hi all,
 
 I would like to know what you consider to be the ideal
 refinement for a
 topology created by ATB ?
 How far should we go in the manual refinement ?
 
 For instance, ATB gave me a topology for a molecule with an
 unsaturated
 acyl chain. Here are some potential issues with this
 topology:
 
 1) Three methyl groups at the end of the acyl chain (that
 are "3 methyl
 groups away" from a double bond) carry a small charge (with
 a net group
 charge of 0, however)
 2) For the double bonds, parameters are "new parameters"
 (not found in
 ffbonded.itp file)
 3) Some bonded parameters in the ATB topology do exist in
 ffbonded.itp file
 but are not supposed to be applied for this kind of bond
 (example: O - S
 bond parameters are written for a C (involved in a double
 bond) - CH2 bond)
 
 My "instinctive" behavior would be to:
 
 1) Put a 0 charge to these methyl groups since they should
 not be charged
 imo
 2) Look for another gromos53a6 topology that includes a
 double bond (like
 this one https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html)
 and take
 the double bond parameters from it
 3) Replace those bonds by correct "default parameters" found
 in
 ffbonded.itp file, in this case by a "C, CHn - C, CHn"
 bonded parameter.
 
 However, I don't wish to break an "equilibrium" that ATB
 could have built
 with some apparently weird parameters.
 
 Hence, is it better to take the ATB topology as it comes, or
 to try to
 refine it ? If the latter, how far should we go ? Isn't it
 risky or
 complicated to justify (in a reviewing process, for example
 :)) ?
 
 Thank you !
 
 
 ------------------------------
 
 Message: 2
 Date: Fri, 16 Dec 2016 12:59:29 +0000
 From: "Nash, Anthony" <a.nash at ucl.ac.uk>
 To: "gmx-users at gromacs.org"
 <gmx-users at gromacs.org>
 Subject: Re: [gmx-users] CG Lincs errors
 Message-ID: <D479947E.15F3F%uccaja0 at ucl.ac.uk>
 Content-Type: text/plain; charset="utf-8"
 
 Hi Peter, 
 
 Thanks for the reply, I know we spoke in length on this
 mater only just
 recently. Many thanks for that.
 
 I?ve taken the time step of collagen in vacu down to 0.0001
 and I?ve
 dropped the temp down to 280. I hope, running over 16 cores
 for two days
 that this should relieve any tension in the backdone before
 in gradually
 increase to 20-40fs. Again, all in vacu with no solvent.
 
 I?ve actually thought about writing a script to modify the
 equilibrium
 bond angles in the CG.itp file for the backbone, using the
 atomistic
 structure as a template. After all, true collagen does not
 replicate
 ?ideal? collagen along the stretch of the protein e.g., the
 MMP1 binding
 site is not very tightly coiled. Perhaps, there lies my
 problem.
 
 I haven?t thought too much of the actual full fibril
 structure, I want to
 capture the D-band gap in  type I collagen. When I give
 it some more
 thought I will probably look into semi-isotropic pressure
 coupling first.
 
 Thanks
 Anthony 
 
 Dr Anthony Nash
 Department of Chemistry
 University College London
 
 Skeletal Tissue Dynamics Group
 Committee member of London Matrix Group @LondonMatrixGrp
 
 
 
 
 
 On 16/12/2016 09:02, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
 on
 behalf of Peter Kroon" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
 on behalf of p.c.kroon at rug.nl>
 wrote:
 
 >As a note to Alex (and the rest of the list), the
 coarse-grained Martini
 >forcefield is usually run with timesteps between 20-40
 fs. 15fs is
 >already rather low. I do agree that longer equilibration
 at low timestep
 >(5 or 10) might help.
 >
 >Alternatively, Do you think a semiisotropic pressure
 coupling might be
 >applicable in this case, since it's an infinite collagen
 polymer?
 >
 >
 >Peter (PhD in the Martini group)
 >
 >
 >On 16-12-16 00:21, Nash, Anthony wrote:
 >> Alex and Mark, thanks for the information. I?ll
 drop dt down,
 >> significantly, drop the temperature, and run it for
 a long time.
 >>
 >> Thanks for the ideas.
 >> Anthony 
 >>
 >>
 >> On 15/12/2016 21:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
 >>on
 >> behalf of Alex" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
 on
 >> behalf of nedomacho at gmail.com>
 wrote:
 >>
 >>> Mark is right, no two ways about it. For
 initial equilibration and
 >>> assessing preexisting structural strains try
 vacuum, _much_ smaller
 >>> timesteps and possibly low temperatures in
 vacuum, only then transfer
 >>>to
 >>> solvent, etc. Algorithmically, LINCS requires
 convergence and you
 >>>already
 >>> are using a pretty high LINCS order... From
 what I see, dt = 15 fs at
 >>>310K
 >>> looks like a cowboy mode simulation in this
 case.
 >>>
 >>> Alex
 >>>
 >>> On Thu, Dec 15, 2016 at 2:32 PM, Mark Abraham
 >>><mark.j.abraham at gmail.com>
 >>> wrote:
 >>>
 >>>> Hi,
 >>>>
 >>>> If a simulation isn't stable with a small
 time step (as I think you
 >>>>are
 >>>> saying) then moving to a larger time step
 is guaranteed to make that
 >>>> worse.
 >>>> Try an even smaller time step, for a long
 time, and see what happens.
 >>>>Or
 >>>> take a subset of your protein and see what
 happens. Or simulate in
 >>>>vacuo
 >>>> for a while. Your topology could be
 unsuited to your starting
 >>>>structure,
 >>>> e.g. some part is under a lot of tension
 that gets released at some
 >>>> point
 >>>> and no finite time step can in practice
 deal with the velocity of the
 >>>> recoil...
 >>>>
 >>>> Mark
 >>>>
 >>>> On Thu, 15 Dec 2016 23:06 Nash, Anthony
 <a.nash at ucl.ac.uk>
 wrote:
 >>>>
 >>>>> Hi all,
 >>>>>
 >>>>> I?m hoping for some help. I?m very
 sorry, this is a bit of a long
 >>>>>one.
 >>>>>
 >>>>> I?ve been struggling for almost a month
 trying to run a CG
 >>>> representation
 >>>>> of our all-atom model of a collagen
 protein (3 polypeptide chains in
 >>>>>a
 >>>>> protein). Our original AMBER all-atom
 model had been successful
 >>>> modelling
 >>>>> using MD. I went on to use the latest
 version of Martinize.py with
 >>>>>the
 >>>>> latest version of the MARTINI
 forcefield fields.
 >>>>>
 >>>>> After a little tweaking (the way AMBER
 names histidine residues), I
 >>>>> successful converted the molecule
 (approx 3100 amino acids) into a CG
 >>>>> representation. I successfully energy
 min the protein in vacuum to a
 >>>>> threshold of 500, and in solvent to a
 threshold of 750 using steepest
 >>>>> descent. Looking for a system at an
 energy min of a threshold around
 >>>> 300
 >>>> I
 >>>>> begin to see LINCS warnings. Observing
 the initial structure, there
 >>>>>is
 >>>>> nothing obviously wrong with the bond
 network (both protein and
 >>>> polarized
 >>>>> CG water).
 >>>>>
 >>>>> I take the system that energy mins at
 750 (protein-water mix, with no
 >>>>> fault reported), and went straight to
 NPT, 20fs step. Blew up. After
 >>>>>a
 >>>> bit
 >>>>> of chatting with the MARTINI community,
 I?ve started with an NVT
 >>>> ensemble,
 >>>>> beginning at 5s then through 10fs,
 15fs, and 20fs. I only run for
 >>>>>1000
 >>>>> steps before switching. Keeping any of
 the simulations running for
 >>>> longer
 >>>>> throws lincs warnings followed by a
 segmentation fault from the
 >>>> warning:
 >>>>> "3 particles communicated to PME rank 7
 are more than 2/3 times the
 >>>>> cut-off out of the domain decomposition
 cell of their charge group in
 >>>>> dimension x."
 >>>>>
 >>>>> Observing the trajectories of any of
 the extended simulations shows
 >>>> the
 >>>>> protein snapping like a rope, and
 always at the same place. I have
 >>>> watched
 >>>>> every trajectory at this point, using
 numerous energy min start
 >>>> points,
 >>>> to
 >>>>> try and understand why it is blowing
 up. I can?t see any obvious
 >>>> reason.
 >>>> I
 >>>>> was told to consider how the
 temperature is changing. Below is an
 >>>> example
 >>>>> of the temperature and pressure from an
 NPT of 20fs step continued
 >>>> from
 >>>>> the very short 20fs step NVT simulation
 (hoping that perhaps CG
 >>>> without
 >>>>> pressure just doesn?t behave happily; I
 was wrong).
 >>>>>
 >>>>>
 >>>>> TEMP:
 >>>>> ?
 >>>>> 6.630000  311.000336
 >>>>>     6.645000 
 311.371643
 >>>>>     6.660000 
 311.724213
 >>>>>     6.675000 
 313.878693
 >>>>>     6.690000 
 681558.937500
 >>>>>
 >>>>>
 >>>>> PRESSURE:
 >>>>> ?
 >>>>> 6.630000    3.559879
 >>>>>     6.645000 
   3.901433
 >>>>>     6.660000 
   3.589078
 >>>>>     6.675000 
   4.158611
 >>>>>     6.690000 
 81762.437500
 >>>>>
 >>>>> The final LINCS warning from this same
 run:
 >>>>>
 >>>>> Step 300, time 4.5 (ps)  LINCS
 WARNING
 >>>>> relative constraint deviation after
 LINCS:
 >>>>> rms 0.000035, max 0.003386 (between
 atoms 2125 and 2126)
 >>>>> bonds that rotated more than 45
 degrees:
 >>>>>  atom 1 atom 2  angle 
 previous, current, constraint length
 >>>>>   
 2125   2126   68.3 
   0.2781   0.2691     
 0.2700
 >>>>>   
 2125   2127   45.9 
   0.2789   0.2701     
 0.2700
 >>>>>
 >>>>>
 >>>>> At this stage the structure ruptures as
 described above.
 >>>>>
 >>>>>
 >>>>> My NVT settings (with NPT included to
 save space) are:
 >>>>>
 >>>>> -----------------
 >>>>> title         
           = Martini
 >>>>>
 >>>>> integrator       
        = md
 >>>>> dt         
              =
 0.015
 >>>>> nsteps       
            = 1000
 >>>>> nstcomm       
           = 100
 >>>>> ;comm-grps       
            
    =
 >>>>>
 >>>>> nstxout       
           = 1000
 >>>>> nstvout       
           = 1000
 >>>>> nstfout       
           = 0
 >>>>> nstlog       
            = 1
 >>>>> nstenergy       
         = 1
 >>>>> nstxout-compressed   
    = 0
 >>>>>
 compressed-x-precision   = 0
 >>>>> ;compressed-x-grps     
   =
 >>>>> energygrps       
        = collagen solvent
 >>>>>
 >>>>> cutoff-scheme     
       = Verlet
 >>>>> nstlist       
           = 20
 >>>>> ns_type       
           = grid
 >>>>>
 >>>>> pbc         
             = xyz
 >>>>> verlet-buffer-tolerance  = 0.005
 >>>>>
 >>>>> coulombtype       
       = PME ;reaction-field
 >>>>> rcoulomb       
          = 1.1
 >>>>> fourierspacing   
    = 0.16 ;0.2  ;0.12
 >>>>>
 >>>>> epsilon_r       
         = 2.5 ;15      ;
 2.5 (with polarizable
 >>>>>water)
 >>>>> epsilon_rf       
        = 0
 >>>>> vdw_type       
          = cutoff
 >>>>> vdw-modifier       
      = Potential-shift-verlet
 >>>>> rvdw         
            = 1.1
 >>>>>
 >>>>> tcoupl       
            = v-rescale
 ;berendsen ;v-rescale
 >>>>> tc-grps       
           = collagen solvent
 >>>>> tau_t         
           = 0.5 0.5 ;1.0 1.0
 >>>>> ref_t         
           = 310 310
 >>>>>
 >>>>> Pcoupl       
            =
 berendsen   ;parrinello-rahman
 >>>>> Pcoupltype       
        = isotropic
 >>>>> tau_p         
           = 12.0  ;
 parrinello-rahman is more stable
 >>>> with
 >>>>> larger tau-p, DdJ, 20130422
 >>>>> compressibility     
     = 10e-4
 >>>>> ref_p         
           = 1.0
 >>>>> refcoord_scaling     
    = com
 >>>>>
 >>>>> gen_vel       
           = no
 >>>>> gen_temp       
          = 310
 >>>>> gen_seed       
          = 473529
 >>>>>
 >>>>> continuation = yes
 >>>>> constraints       
       = none
 >>>>> constraint_algorithm 
    = lincs
 >>>>> lincs-warnangle = 45
 >>>>> lincs-order=8
 >>>>> lincs-iter=4
 >>>>>
 >>>>>
 >>>>> ??????????
 >>>>>
 >>>>> Every setting bar the lincs iter,
 order, warnangle were supplied with
 >>>> the
 >>>>> latest version of MARTINI. During many
 NVT runs I have adjusted the
 >>>> tau-t
 >>>>> to try and keep the thermostat from
 oscillating its way into
 >>>>>infinity.
 >>>>>
 >>>>> I?m curious, will an out of control
 thermostat break a structure, or
 >>>> will
 >>>>> a structure breaking (for what ever
 reason this structure is
 >>>>>breaking)
 >>>>> cause the thermostat to go out of
 control?
 >>>>>
 >>>>> My only thought thought is the initial
 .itp file that Martinize
 >>>> created.
 >>>> I
 >>>>> informed the script that this was
 collagen, therefor it sets ?F? and
 >>>> the
 >>>>> corresponding bonded parameters. A
 human collagen is not perfect in
 >>>> its
 >>>>> helical structure. Could there be
 underlying forces contributed from
 >>>> badly
 >>>>> bonded backbone-backbone arrangements?
 >>>>>
 >>>>> [ atoms ]
 >>>>>     1   
 N0     1   GLY 
   BB     1  0.0000 ; F
 >>>>>     2   
 N0     2   LEU 
   BB     2  0.0000 ; F
 >>>>>     3   
 C1 
    2   LEU   SC1 
    3  0.0000 ; F
 >>>>>     4   
 N0     3   SER 
   BB     4  0.0000 ; F
 >>>>>
 >>>>>
 >>>>> Many thanks
 >>>>> Anthony
 >>>>>
 >>>>> Thanks
 >>>>> Anthony
 >>>>>
 >>>>> --
 >>>>> 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!
 >>>>
 >>>> * 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!
 >>>
 >>> * 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: Fri, 16 Dec 2016 16:26:10 -0500
 From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org
 Subject: Re: [gmx-users] Desolvation or hydration free
 energy of an
     ION
 Message-ID: <5bc664fd-1288-bf34-b57f-68103f4bea88 at vt.edu>
 Content-Type: text/plain; charset=windows-1252;
 format=flowed
 
 
 
 On 12/15/16 10:15 AM, Alex wrote:
 > Thanks Justin for your response.
 >
 > Surly PMF is better, but the point is that via FEP I
 have already calculate
 > the binding free energy of a charged amino acid to a
 solid surface while
 > Na+ used as counter-ion where both "amino acid and Na+"
 considered as a
 > single "couple-moltype" to be decoupled both of them
 simultaneously from
 > the system. And of course by this I have desolvation
 energy of Na+ into
 > account which should not be. So, I want to calculate
 the desolvation energy
 > of only Na+ to remove its portion out from my original
 calculation. That is
 > why I want to keep the conditions as my original
 simulations.
 >
 >  With free energy of {amino acid and Na+} in both
 bounded and unbounded to
 > the solid slab, I mean DG_unbounded{AA and Na+} -
 DG_bounded{AA and Na+},
 > the portion of Na+ has been already removed partially,
 but not completely.
 >
 
 Are there significant interactions between the amino acid
 and Na+, and/or the 
 surface and Na+? If so, the only way to figure out the
 extent of the 
 contribution is a full thermodynamic cycle in which the
 amino acid and Na+ are 
 decoupled separately.
 
 -Justin
 
 > Regards,
 > Alex
 >
 > On Thu, Dec 15, 2016 at 3:55 PM, Justin Lemkul <jalemkul at vt.edu>
 wrote:
 >
 >>
 >>
 >> On 12/15/16 9:39 AM, Alex wrote:
 >>
 >>> Hello gromacs user,
 >>>
 >>> I was wondering if anybody has experience with
 the hydration or
 >>> desolvation
 >>> free energy of an ION for example Na+, using
 alchemical free energy
 >>> perturbation method?
 >>>
 >>> Actually in my case, I would like to calculate
 the difference between free
 >>> energy of "Na+" when it is close to a solid
 slab in aqueous solutions,
 >>> and
 >>> when it is far away from the slab inside bulk
 water.
 >>>
 >>>
 >> If it's a simple matter of Na+ partially
 desolvating to bind to the
 >> surface (with no intervening waters) then the
 simple approach is a PMF.
 >> Using a decoupling method requires additional
 restraints that have to be
 >> accounted for. This can of course be done done but
 a PMF is trivial to set
 >> up.
 >>
 >> -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
 >>
 >> ==================================================
 >> --
 >> 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.
 >>
 
 -- 
 ==================================================
 
 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
 
 ==================================================
 
 
 ------------------------------
 
 -- 
 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.
 
 End of gromacs.org_gmx-users Digest, Vol 152, Issue 55
 ******************************************************
 


More information about the gromacs.org_gmx-users mailing list