[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:
>Send gmx-users mailing list submissions to
>	gmx-users at gromacs.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://lists.gromacs.org/mailman/listinfo/gmx-users
>or, via email, send a message with subject or body 'help' to
>	gmx-users-request at gromacs.org
>
>You can reach the person managing the list at
>	gmx-users-owner at gromacs.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gmx-users digest..."
>
>
>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
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100613/c82201e3/attachment-0001.html
>
>------------------------------
>
>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
> 
> 
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100613/5c69634e/attachment-0001.html
>
>------------------------------
>
>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>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Skipped content of type multipart/alternative-------------- next part --------------
>A non-text attachment was scrubbed...
>Name: NAD.mol2
>Type: application/octet-stream
>Size: 7048 bytes
>Desc: not available
>Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20100613/2683a19c/NAD.obj
>-------------- next part --------------
>A non-text attachment was scrubbed...
>Name: NAD.png
>Type: image/png
>Size: 9695 bytes
>Desc: not available
>Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20100613/2683a19c/NAD.png
>
>------------------------------
>
>-- 
>gmx-users mailing list
>gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>
>End of gmx-users Digest, Vol 74, Issue 73
>*****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100614/b64921a3/attachment.html>


More information about the gromacs.org_gmx-users mailing list