[gmx-users] Re:gmx-users Digest, Vol 74, Issue 73
fancy2012
fancy2012 at yeah.net
Mon Jun 14 12:43:49 CEST 2010
Dear all,
Thanks very much for Justin A. Lemkul's explanations! I have got the idea.
I have a problem of my mailing list, I can't receive the independent mails from mailing list as before. I can only get the Digest, is there something wrong with my e-mail box? Thanks very much!
All the best,
fancy
在2010-06-14，gmx-users-request at gromacs.org 写道：
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>Today's Topics:
>
> 1. epsilon_r (fancy2012)
> 2. soft-core (fancy2012)
> 3. Re: Andersen thermostat (Justin A. Lemkul)
> 4. Re: epsilon_r (Justin A. Lemkul)
> 5. Re: soft-core (Justin A. Lemkul)
> 6. Adding Partial Charges for Small Molecules (Nancy)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Sun, 13 Jun 2010 18:59:51 +0800 (CST)
>From: fancy2012 <fancy2012 at yeah.net>
>Subject: [gmx-users] epsilon_r
>To: gmx-users <gmx-users at gromacs.org>
>Message-ID: <6db141e8.4de3.12930f729e2.Coremail.fancy2012 at yeah.net>
>Content-Type: text/plain; charset="gbk"
>
>Dear GMX users,
>
>I find this parameter epsilon_r in a tutorial of free energy calculation, but I don't know its meaning. And also I can't find it in the manual of version 4. Could somebody explain it for me? Thanks very much!
>
>All the best,
>fancy
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>------------------------------
>
>Message: 2
>Date: Sun, 13 Jun 2010 19:14:24 +0800 (CST)
>From: fancy2012 <fancy2012 at yeah.net>
>Subject: [gmx-users] soft-core
>To: gmx-users <gmx-users at gromacs.org>
>Message-ID: <7fc8ee26.4ec3.12931047b26.Coremail.fancy2012 at yeah.net>
>Content-Type: text/plain; charset="gbk"
>
>Dear GMX users,
>when I generate the input file of MD simulation using grompp, I get this error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know how to figure it out? Could somebody give me a hand? Thanks very much in advance!
>Here is the mdp file:
>cpp = /lib/cpp
>constraints = all-bonds
>integrator = md
>tinit = 0.0
>dt = 0.002
>nsteps = 25000
>nstcomm = 1
>nstxout = 10000
>nstvout = 0
>nstfout = 0
>nstlog = 500
>nstenergy = 250
>nstxtcout = 1000
>xtc_precision = 1000
>xtc_grps = Protein
>nstlist = 5
>energygrps = Protein SOL
>ns_type = grid
>rlist = 0.9
>coulombtype = Reaction-Field
>epsilon_r = 78.0
>rcoulomb = 1.4
>rvdw = 1.4
>Tcoupl = Berendsen
>tc-grps = Protein SOL
>ref_t = 300 300
>tau_t = 0.1 0.1
>Pcoupl = Berendsen
>tau_p = 1.0
>compressibility = 4.6e-5
>ref_p = 1.0
>free_energy = yes
>init_lambda = 0.00
>sc-alpha = 1.51
>
>All the best,
>fancy
>
>
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>------------------------------
>
>Message: 3
>Date: Sun, 13 Jun 2010 19:53:28 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] Andersen thermostat
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4C156F78.5050907 at vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>Sai Pooja wrote:
>> Hi,
>>
>> I want to use the Andersen Thermostat (not v-rescale). But I get an
>> error when I try to use it. My mdp file is as below:
>>
>
>My guess is that the error stems from the fact that the Andersen thermostat has
>not been implemented in Gromacs. Manual section 7.3.14.
>
>-Justin
>
>> title =NPT simulation for a 2D WCA system
>> cpp =/lib/cpp
>>
>> ; RUN CONTROL PARAMETERS
>> integrator = md
>> dt = 0.0005
>> nsteps = 400
>>
>> ; OUTPUT CONTROL OPTIONS
>> nstxout = 50 ; No output, except for last frame
>> (coordinates)
>> nstvout = 0 ; No output, except for last frame
>> (velocities)
>> nstfout = 0 ; No output, except for last frame (forces)
>> nstlog = 100 ; Write every nth step to the log
>> nstenergy = 100 ; Write energies at every n step
>> nstxtcout = 0 ; Do not write a compressed tr
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> nstlist = 10
>> ns-type = Grid
>> pbc = xyz
>> rlist = 0.9
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> coulombtype = Cut-off
>> rcoulomb = 1.1225
>> vdw-type = Cut-off
>> rvdw = 1.1225
>>
>> ; Temperature coupling
>> tcoupl = Andersen
>> tc-grps = ARAR
>> tau_t = 0.1
>> ref_t = 120.2717
>> andersen_seed =-1
>>
>> ; Pressure coupling
>> pcoupl = Berendsen
>> pcoupltype = semiisotropic
>> tau-p = 0.20 0.20
>> compressibility = 1e-5 0 ;Dont know
>> ref-p = 50 0
>>
>>
>> ;Generate velocities for startup run
>> gen_vel =yes
>> gen_temp =120.2717
>> gen_seed =-1
>>
>> ;Constraints
>> constraints = all-bonds
>> constraint_algorithm = LINCS
>> lincs_order = 4
>> lincs_iter = 1
>> lincs_warnangle = 90
>> ;unconstrained_start = no
>> ;shake_tol = 0.0001
>>
>>
>>
>> Any idea why this would not work?
>>
>> Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
>
>Message: 4
>Date: Sun, 13 Jun 2010 19:55:13 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] epsilon_r
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4C156FE1.3010100 at vt.edu>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
>fancy2012 wrote:
>> Dear GMX users,
>>
>> I find this parameter epsilon_r in a tutorial of free energy
>> calculation, but I don't know its meaning. And also I can't find it in
>> the manual of version 4. Could somebody explain it for me? Thanks very much!
>>
>
>Well, it's certainly in the manual - section 7.3.10.
>
>-Justin
>
>> All the best,
>> fancy
>>
>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
>
>Message: 5
>Date: Sun, 13 Jun 2010 19:56:36 -0400
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] soft-core
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4C157034.70404 at vt.edu>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
>fancy2012 wrote:
>> Dear GMX users,
>> when I generate the input file of MD simulation using grompp, I get this
>> error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't
>> know how to figure it out? Could somebody give me a hand? Thanks very
>> much in advance!
>
>You haven't specified a value for sc-power, so the default of zero is taken.
>Manual section 7.3.23.
>
>-Justin
>
>> Here is the mdp file:
>> cpp = /lib/cpp
>> constraints = all-bonds
>> integrator = md
>> tinit = 0.0
>> dt = 0.002
>> nsteps = 25000
>> nstcomm = 1
>> nstxout = 10000
>> nstvout = 0
>> nstfout = 0
>> nstlog = 500
>> nstenergy = 250
>> nstxtcout = 1000
>> xtc_precision = 1000
>> xtc_grps = Protein
>> nstlist = 5
>> energygrps = Protein SOL
>> ns_type = grid
>> rlist = 0.9
>> coulombtype = Reaction-Field
>> epsilon_r = 78.0
>> rcoulomb = 1.4
>> rvdw = 1.4
>> Tcoupl = Berendsen
>> tc-grps = Protein SOL
>> ref_t = 300 300
>> tau_t = 0.1 0.1
>> Pcoupl = Berendsen
>> tau_p = 1.0
>> compressibility = 4.6e-5
>> ref_p ; = 1.0
>> free_energy = yes
>> init_lambda = 0.00
>> sc-alpha = 1.51
>> All the best,
>> fancy
>>
>>
>>
>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>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: Sun, 13 Jun 2010 20:44:32 -0400
>From: Nancy <nancy5villa at gmail.com>
>Subject: [gmx-users] Adding Partial Charges for Small Molecules
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
> <AANLkTimFLvxqbiO-d6ddWNyLTn_tJuZtIKDRR5JkoSvt at mail.gmail.com>
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