[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 24 00:09:36 CEST 2008
shahrbanoo karbalaee wrote:
> 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)?
There is no substitute for a thorough examination of the literature.
> AND about this file :
> it is md after equilbration.
Then gen_vel = yes just negated your equilibration. Whether or not that will
cause any problems will become obvious if your simulation crashes.
-Justin
>
> 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
>>
>> ========================================
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>>
>> End of gmx-users Digest, Vol 51, Issue 85
>> *****************************************
>>
>
>
--
========================================
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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