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-requ...@gromacs.org 写道: >Send gmx-users mailing list submissions to > gmx-users@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-requ...@gromacs.org > >You can reach the person managing the list at > gmx-users-ow...@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 <fancy2...@yeah.net> >Subject: [gmx-users] epsilon_r >To: gmx-users <gmx-users@gromacs.org> >Message-ID: <6db141e8.4de3.12930f729e2.coremail.fancy2...@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 <fancy2...@yeah.net> >Subject: [gmx-users] soft-core >To: gmx-users <gmx-users@gromacs.org> >Message-ID: <7fc8ee26.4ec3.12931047b26.coremail.fancy2...@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" <jalem...@vt.edu> >Subject: Re: [gmx-users] Andersen thermostat >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4c156f78.5050...@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" <jalem...@vt.edu> >Subject: Re: [gmx-users] epsilon_r >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4c156fe1.3010...@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" <jalem...@vt.edu> >Subject: Re: [gmx-users] soft-core >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4c157034.70...@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 <nancy5vi...@gmail.com> >Subject: [gmx-users] Adding Partial Charges for Small Molecules >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: > <aanlktimflvxqbio-d6ddwnyltn_tjuztikdrr5jko...@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@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 >*****************************************
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