[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85
shahrbanoo karbalaee
shahrbanoo at gmail.com
Wed Jul 23 19:24:14 CEST 2008
Dear justin
thank you for your help and answer.
about NVT or NPT,what is generally use for peptide?are there more
different between them if iI can use NPT in our
output(flexiblity)?
AND about this file :
it is md after equilbration.
thanks again
best regard
karbalaee
> ------------------------------
>
> Message: 3
> Date: Wed, 23 Jul 2008 18:14:50 +0430
> From: "shahrbanoo karbalaee" <shahrbanoo at gmail.com>
> Subject: [gmx-users] Is it correct
> To: gmx-users at gromacs.org
> Message-ID:
> <63e46fea0807230644gec76718u6cc2198eeea12b61 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear justin
> In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
> say me Is that correct.
>
> title = cpeptide MD
> cpp = /lib/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 5 ps.
> nstcomm = 1
> nstxout = 50
> nstvout = 0
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc-grps = protein sol
> ref_t = 300 300
> ; Pressure coupling is not on
> Pcoupl = no
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> --
> 2)In the place program doesent have phrase for example PME,....does.
> the gromacs use default?
> 3)when I use berendsen coupling is on and pcoup =yes and In my work is
> effect in fluctuate?
>
> best
> sh-karbalaee
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 23 Jul 2008 13:54:57 +0000 (GMT)
> From: Claus Valka <lastexile7gr at yahoo.de>
> Subject: Re : [gmx-users] switch potential function gromacs 3.3.2
> To: gmx-users at gromacs.org
> Message-ID: <65108.96571.qm at web26602.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Sir or Madam,
>
> For the version 3.3.2 the gromacs switch potential function is the following :
>
> Elja1 = (4.d0*eps1*sig1**6) * &
> -(1.d0/r(i)**6) * &
> (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &
> + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &
> - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)
> Elja2 = (4.d0*eps1*sig1**12) * &
> (1.d0/r(i)**12) * &
> (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &
> + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &
> - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)
>
> Switch = Elja1 + Elja2
>
> Remarks:
> i) This is tested only when in the mdp file the vdw-type = Switch
> ii) The Elja1 is the dispersion part of the potential (not the force).
> iii) The Elja2 it the repulsion part of the potential (not the force).
> iv) eps is the value of epsilon and sig is the value of sigma
> v) r1 = rvdw-switch and rc1 = rvdw
> vii) The function of the manual that sais that it applies Phi(r) both on switch and shift option doesn't seem to apply in the switch case.
> vii) Someone can find out if someone searches at : a)/root/Desktop/software/gromacs/gromacs-3.3.2/src/mdlib/
> b)The file is called tables.c
> c)look under if (bSwitch), where it sais swi
> d)for pow look at the beginning
> e)for Vtab under the cases etabLJ6 and etabLJ12
> f)for whole under if ((r_r1) && bSwitch) , that is the multiplication of the dispersion and repulsion part with swi
> g)in order to have units of energy someone must to multiply the above with 4*epsilon*sigma**6 for the dispersion part and 4*epsilon*sigma**12 for the repulsion part
>
> Yours Sincerely,
> Nikos
>
>
>
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> ------------------------------
>
> Message: 5
> Date: Wed, 23 Jul 2008 09:58:14 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] new version of C terminus database for charmm
> To: sarbani chattopadhyay <sarbani_c84 at rediffmail.com>, Discussion
> list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <488738F6.2010009 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sarbani chattopadhyay wrote:
> >
> > Hi,
> > I am trying to run gromacs with charmm forcefield.
> > # I had run the perl program "convert_charmm_to_gromacs.pl" and put the
> > output files
> > "ffcharmmbon.itp" and "ffcharmmnb.itp" into the gromacs
> > share/gromacs/top directory.
> >
> > # I had put all the files from the "tar" file into the share/gromacs/top
> > directory.
> >
> > # I had updated the "FF.dat" file to include the charmm file.
> >
> > # I undersatand that the format of the termini database have changed for
> > the 3.3.2 version.
> > I could make the changes in "ffcharmm-n.tdb".
> >
> > Accordingly I tried to make the changes in "ffcharmm-c.tdb", but when I
> > give the command
> > pdb2gmx -f 1aoc.gro -ff charmm -ter
> > I get the following error
> > Reading Termini Database: expected 3 items of atom data in stead of 1 on
> > line
> > O OC 15.9994 -0.670
> > I guess the ffcharmm-c.tdb file has not been changed correctly.Has
> > anyone done it?
> > I will be grateful if someone can help me in this.
> >
>
> This was a strange error; I remember coming across it as well. No modification
> that I could make to that line alleviated the problem, and I still don't know
> why. What I ended up doing was changing the [ COO- ] section to the following:
>
> [ COO- ]
> [ replace ]
> C CC 12.0110 0.340
> [ add ]
> 2 8 O C CA N
> OC 15.999 -0.670
> [ delete ]
> O
> [ impropers ]
> C CA O2 O1 improper_OB_X_X_CD_
>
> Therefore, instead of replacing O by OC, the O is deleted, and an OC added back
> in its place. I don't know why that works, and the "replace" function doesn't,
> so maybe someone else has a better idea, but this is how I got around it.
>
> -Justin
>
> > Thanks in advance
> > Sarbani
> >
> >
> >
> > Rediff Shopping
> > <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 23 Jul 2008 10:04:36 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Is it correct
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48873A74.5040102 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> shahrbanoo karbalaee wrote:
> > Dear justin
> > In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
> > say me Is that correct.
>
> The definition of "correct" is up to you. I'll give you a few pointers
> (embedded below), but the leg-work of determining the validity of the parameters
> is your homework, not mine (or anyone else's!)
>
> >
> > title = cpeptide MD
> > cpp = /lib/cpp
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 5000 ; total 5 ps.
> > nstcomm = 1
> > nstxout = 50
> > nstvout = 0
>
> Are you sure you don't want to save velocities every now and again? If your run
> crashes because of a hardware problem, you may want to be able to restart it...
>
> What about using nstxtcout? The output file will be greatly compressed relative
> to the .trr. It will save a lot of disk space when running analysis.
>
> > nstfout = 0
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
>
> All of the parameters from nstlist to rvdw have values that are generally
> determined by the force field and its derivation scheme. Check the literature.
>
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = berendsen
> > tau_t = 0.1 0.1
> > tc-grps = protein sol
> > ref_t = 300 300
>
> As long as you have no ions this is fine.
>
> > ; Pressure coupling is not on
> > Pcoupl = no
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
>
> As long as you are expecting an NVT ensemble, this is also fine.
>
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
>
> Is this .mdp file for equilibration or production? You refer to it as the
> md.mdp, but if you're re-generating velocities, I certainly hope this .mdp file
> is for the beginning of equilibration. If you re-generate velocities
> repeatedly, then you don't get a continuous trajectory.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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> gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 51, Issue 85
> *****************************************
>
--
sh-karbalaee
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