[gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 157

Tue Jul 12 06:54:19 CEST 2016

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Muhammad Tahir Ayub
Junior Research Fellow
Lab No.  P-133, Computational Chemistry Unit,
Dr. Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN: (92-21) 111-222-292 Ext. (309)
E-mail: tahirgp0 at gmail.com
http://sites.google.com/site/zaheerqasmi/groupmember

On Wed, Jun 29, 2016 at 9:55 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Diffusion constant (pari lotfi)
>    2. Re: Diffusion constant (Mark Abraham)
>    3. Water molecule can not be settled (zeineb SI CHAIB)
>    4. Re: Water molecule can not be settled (Mark Abraham)
>    5. Re: Water molecule can not be settled (Mark Abraham)
>    6. Re: Tesla K80 vs GeForce GTX 980-repost (Szil?rd P?ll)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Jun 2016 19:42:54 +0430
> From: pari lotfi <bentolhoda.lotfi at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Diffusion constant
> Message-ID:
>         <CAJ8wd6aVViqJgjdmQMaqZP=
> B1+M6PCNFj71VoGT_C9FLchomdg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> what is the meaning of this statement?
>
> "The diffusion constant is calculated by least squares fitting a straight
> line (D*t + c) through the MSD(t) from -beginfit to -endfit (note that t is
> a time from the reference positions, not simulation time)."
>
> I calculated diffusion constant of the water in a simulation by Gromacs 4.5
> and I write a c++ code for calculation of diffusion constant. Unfortunately
> diffusion constant of c++ code and "g_msd" not equal.
>
> I think the meaning of above statement helps me.
>
> Thanks in advance,
> Pari
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 29 Jun 2016 15:21:55 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Diffusion constant
> Message-ID:
>         <
> CAMNuMARJqzSfNAK1x0QSQQEnCVFcXc6SuLZW6HJ7s+9_9HtP2A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Which aspect isn't clear?
>
> Mark
>
> On Wed, 29 Jun 2016 17:13 pari lotfi <bentolhoda.lotfi at gmail.com> wrote:
>
> > Dear all,
> >
> > what is the meaning of this statement?
> >
> > "The diffusion constant is calculated by least squares fitting a straight
> > line (D*t + c) through the MSD(t) from -beginfit to -endfit (note that t
> is
> > a time from the reference positions, not simulation time)."
> >
> > I calculated diffusion constant of the water in a simulation by Gromacs
> 4.5
> > and I write a c++ code for calculation of diffusion constant.
> Unfortunately
> > diffusion constant of c++ code and "g_msd" not equal.
> >
> > I think the meaning of above statement helps me.
> >
> > Thanks in advance,
> > Pari
> > --
> > 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: Wed, 29 Jun 2016 16:26:49 +0100
> From: zeineb SI CHAIB <zeineb-14 at hotmail.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Water molecule can not be settled
> Message-ID: <DUB119-W18E3DBCB426B00740A8A13F8230 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx users,
>
> I'm having problems during my energy minimisation step, I tried different
> options in the mdp file but I'm enable to fix the problem, I'm hoping that
> you can help me with this.
>
> My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF)
> and arginin (substrate). I'm using CHARMM27 as a force field.
>
> At the beginning I fixed the problem of the HEM (perfectly linked with the
> protein and completed its parameters).
> In the second step, I generated the topology of THF with Swissparam's
> server. I succeeded in running a molecular dynamic of 5ns. When I analysed
> the dynamic the THF was in its right place and I didn't see any anormal
> behaviour with my structure.
>
> Now, I'm trying to include the topology of the THF in CHARMM ff folder in
> order to gain time and make things  more automatic. The modifications that
> I did were:
> - I added the residue to the .rtp file of CHARMM FF, only  [atoms] entry.
> For the other entries [angles], [impropres]..etc, according to GROMACS
> manual, they are optional so I did'nt add them.
>
> - I created an entry for THF in the .hdb file of CHARMM ff.
>
> After that, I run pdb2gmx and it succeeded to generate the topology. The
> global structure looked OK but during energy minimisation, I got this Fatal
> error:
>
> Fatal error:
> step 36: Water molecule starting at atom 15431 can not be settled.
> The atom 15431 belong to a water molecule and is far from the protein!!
>
>
> Here are the parameters that I used in the mdp file:
> integrator = steep
> nsteps = 50000
> nstxout = 1
> ns_type = grid
> energygrps  = Protein THG
> emtol = 1000.0
> emstep = 0.01
>
> ; Non bonded stuff (specific to CHARMM)
> constraints = h-bonds
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 1.0
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
>
> I tried to change the parameters (one changement each time) but it didn't
> work:
> 1- define = DFLEXIBLE
> 2- define = DEPOSRE
> 3- constraints = all-bonds
> 4- emstep = 0,02
>
> I can't see where is the problem! Anyone can help me please.
>
> Regards.
>
> Zeineb
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 29 Jun 2016 15:32:08 +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"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Water molecule can not be settled
> Message-ID:
>         <CAMNuMAQ2O7eppW=17CuLX7Q6yJ3R5f==
> 20RVg7EX3Vsb2ABiEw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> First, minimise your protein in vacuo, so you have some confidence in your
> topology. Then solvate and minimise again. Your problem just looks like a
> standard case of not being gentle enough in an edge case.
>
> Mark
>
> On Wed, 29 Jun 2016 17:27 zeineb SI CHAIB <zeineb-14 at hotmail.com> wrote:
>
> > Dear gmx users,
> >
> > I'm having problems during my energy minimisation step, I tried different
> > options in the mdp file but I'm enable to fix the problem, I'm hoping
> that
> > you can help me with this.
> >
> > My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF)
> > and arginin (substrate). I'm using CHARMM27 as a force field.
> >
> > At the beginning I fixed the problem of the HEM (perfectly linked with
> the
> > protein and completed its parameters).
> > In the second step, I generated the topology of THF with Swissparam's
> > server. I succeeded in running a molecular dynamic of 5ns. When I
> analysed
> > the dynamic the THF was in its right place and I didn't see any anormal
> > behaviour with my structure.
> >
> > Now, I'm trying to include the topology of the THF in CHARMM ff folder in
> > order to gain time and make things  more automatic. The modifications
> that
> > I did were:
> > - I added the residue to the .rtp file of CHARMM FF, only  [atoms] entry.
> > For the other entries [angles], [impropres]..etc, according to GROMACS
> > manual, they are optional so I did'nt add them.
> >
> > - I created an entry for THF in the .hdb file of CHARMM ff.
> >
> > After that, I run pdb2gmx and it succeeded to generate the topology. The
> > global structure looked OK but during energy minimisation, I got this
> Fatal
> > error:
> >
> > Fatal error:
> > step 36: Water molecule starting at atom 15431 can not be settled.
> > The atom 15431 belong to a water molecule and is far from the protein!!
> >
> >
> > Here are the parameters that I used in the mdp file:
> > integrator = steep
> > nsteps = 50000
> > nstxout = 1
> > ns_type = grid
> > energygrps  = Protein THG
> > emtol = 1000.0
> > emstep = 0.01
> >
> > ; Non bonded stuff (specific to CHARMM)
> > constraints = h-bonds
> > cutoff-scheme = Verlet
> > vdwtype = cutoff
> > vdw-modifier = force-switch
> > rlist = 1.2
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > coulombtype = PME
> > rcoulomb = 1.2
> > DispCorr = no
> >
> > I tried to change the parameters (one changement each time) but it didn't
> > work:
> > 1- define = DFLEXIBLE
> > 2- define = DEPOSRE
> > 3- constraints = all-bonds
> > 4- emstep = 0,02
> >
> > I can't see where is the problem! Anyone can help me please.
> >
> > Regards.
> >
> > Zeineb
> >
> > --
> > 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: 5
> Date: Wed, 29 Jun 2016 15:32:08 +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"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Water molecule can not be settled
> Message-ID:
>         <CAMNuMAQ2O7eppW=17CuLX7Q6yJ3R5f==
> 20RVg7EX3Vsb2ABiEw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> First, minimise your protein in vacuo, so you have some confidence in your
> topology. Then solvate and minimise again. Your problem just looks like a
> standard case of not being gentle enough in an edge case.
>
> Mark
>
> On Wed, 29 Jun 2016 17:27 zeineb SI CHAIB <zeineb-14 at hotmail.com> wrote:
>
> > Dear gmx users,
> >
> > I'm having problems during my energy minimisation step, I tried different
> > options in the mdp file but I'm enable to fix the problem, I'm hoping
> that
> > you can help me with this.
> >
> > My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF)
> > and arginin (substrate). I'm using CHARMM27 as a force field.
> >
> > At the beginning I fixed the problem of the HEM (perfectly linked with
> the
> > protein and completed its parameters).
> > In the second step, I generated the topology of THF with Swissparam's
> > server. I succeeded in running a molecular dynamic of 5ns. When I
> analysed
> > the dynamic the THF was in its right place and I didn't see any anormal
> > behaviour with my structure.
> >
> > Now, I'm trying to include the topology of the THF in CHARMM ff folder in
> > order to gain time and make things  more automatic. The modifications
> that
> > I did were:
> > - I added the residue to the .rtp file of CHARMM FF, only  [atoms] entry.
> > For the other entries [angles], [impropres]..etc, according to GROMACS
> > manual, they are optional so I did'nt add them.
> >
> > - I created an entry for THF in the .hdb file of CHARMM ff.
> >
> > After that, I run pdb2gmx and it succeeded to generate the topology. The
> > global structure looked OK but during energy minimisation, I got this
> Fatal
> > error:
> >
> > Fatal error:
> > step 36: Water molecule starting at atom 15431 can not be settled.
> > The atom 15431 belong to a water molecule and is far from the protein!!
> >
> >
> > Here are the parameters that I used in the mdp file:
> > integrator = steep
> > nsteps = 50000
> > nstxout = 1
> > ns_type = grid
> > energygrps  = Protein THG
> > emtol = 1000.0
> > emstep = 0.01
> >
> > ; Non bonded stuff (specific to CHARMM)
> > constraints = h-bonds
> > cutoff-scheme = Verlet
> > vdwtype = cutoff
> > vdw-modifier = force-switch
> > rlist = 1.2
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > coulombtype = PME
> > rcoulomb = 1.2
> > DispCorr = no
> >
> > I tried to change the parameters (one changement each time) but it didn't
> > work:
> > 1- define = DFLEXIBLE
> > 2- define = DEPOSRE
> > 3- constraints = all-bonds
> > 4- emstep = 0,02
> >
> > I can't see where is the problem! Anyone can help me please.
> >
> > Regards.
> >
> > Zeineb
> >
> > --
> > 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: 6
> Date: Wed, 29 Jun 2016 18:54:57 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Tesla K80 vs GeForce GTX 980-repost
> Message-ID:
>         <CANnYEw6wOhKcUVAxe_xiaeM3zjq=ZUNwSVQ+GkzKe51wV6Yy=
> g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Get Geforce unless you have a very good reason to need/want Tesla
> (double prec. or amount memory for other codes is the only thing I can
> think of).
>
> The GROMACS kernels on the 980Ti will be approx 1.5x faster per GPU
> than the K80 per chip (i.e. haf the K80 board) and you'll get faster
> transfers too (more PCI lanes used); in other words, 2x 980Ti will
> easily be faster than a K80 board and it will save you a lot of money.
>
> But why not get 1070s instead?
>
>
> On Mon, Jun 27, 2016 at 7:56 PM, Nikhil Maroli <scinikhil at gmail.com>
> wrote:
> > Hi all,
> >
> > Looking for the best configuration with the processor 2 x Intel? Xeon?
> > E5-2670 v3 (2.3 GHz, 30 MB cache, 12 cores))
> >
> > we have two option
> >
> > 1. Tesla K80
> >
> > 2. 3 x GeForce GTX 980ti (Three cards connect with SLI Bridge and
> achieving
> > good speed which equivalent to K80 )
> >
> >
> >
> > I have found 3 (GTX 980ti )cards cheaper and giving little faster than
> > Tesla K80
>
> Only a little faster? Something must be off!
>
> >,Since its Consumer Card most of the supplier asking me to
> > reconsider it ...
>
> Don't worry about that. For the price of a single K80 you can get a
> few backup GPUs just in case and you'll still have money left ;)
>
> BTW, make sure you get a well cooled server, though!
>
> Cheers,
> --
> Szil?rd
>
> >
> > Looking for the suggestions, Option 1 or Option 2 is best
> > --
> > Regards,
> > Nikhil Maroli
> > --
> > 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.
>
> End of gromacs.org_gmx-users Digest, Vol 146, Issue 157
> *******************************************************
>