Dear Prof. Justin A. Lemkul, Thanks very much for the website you supplied. It is very useful to me! Thank you again!
-- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China At 2011-04-10,gmx-users-requ...@gromacs.org wrote: >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. Re: NPT.mdp parameters NOTE (Peter C. Lai) > 2. Re: converging value (Mark Abraham) > 3. Re: Dangling bond error for dna (Justin A. Lemkul) > 4. probelm of using amber force field (fancy2012) > 5. Re: probelm of using amber force field (Justin A. Lemkul) > 6. Re: converging value (mohsen ramezanpour) > 7. Re: converging value (Mark Abraham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sun, 10 Apr 2011 05:02:10 -0500 >From: "Peter C. Lai" <p...@uab.edu> >Subject: Re: [gmx-users] NPT.mdp parameters NOTE >To: mohsen ramezanpour <ramezanpour.moh...@gmail.com> >Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <20110410100210.gi54...@cesium.hyperfine.info> >Content-Type: text/plain; charset="us-ascii" > >He told me you can use up to 0.5 in an off-list email and in fact, does so >in the KALP-15 in DPPC example... > >On 2011-04-10 02:54:15AM -0500, mohsen ramezanpour wrote: >> Dear Dr.Justin >> >> As you have noticed in your tutorials,It is better to use Nose-Hoover for >> tempreture in the NPT.mdp file. >> You have used tau-t = 0.1 in most of your md.mdp files for generating npt >> ensemble. >> >> When I use a npt file with these settings,there is a Note as following: >> sorry,i can't remember the exact messge but :it says it is better to use a >> tau_t 20 times of another quantity, >> in my work the quantity=0.01 >> >> When I made tau_t=0.2 there was not any Note! >> >> Can I ignore this Note?Is it safe continuing with the same tau_t=0.1 as you >> used? >> > >> -- >> 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/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >-- >=============================================================== >Peter C. Lai | University of Alabama-Birmingham >Programmer/Analyst | BEC 257 >Genetics, Div. of Research | 1150 10th Avenue South >p...@uab.edu | Birmingham AL 35294-4461 >(205) 690-0808 | >=============================================================== > > > >------------------------------ > >Message: 2 >Date: Sun, 10 Apr 2011 20:39:25 +1000 >From: Mark Abraham <mark.abra...@anu.edu.au> >Subject: Re: [gmx-users] converging value >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4da188dd.7090...@anu.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: >> Dear All >> >> How can I determine the converged value of a simulation? >> Because the pressure has big oscilations around it's converging value >> but it is difficult to determine that value. > >Longer simulations on bigger systems. > >Mark > > >------------------------------ > >Message: 3 >Date: Sun, 10 Apr 2011 07:17:59 -0400 >From: "Justin A. Lemkul" <jalem...@vt.edu> >Subject: Re: [gmx-users] Dangling bond error for dna >To: "Gromacs Users' List" <gmx-users@gromacs.org> >Message-ID: <4da191e7.3030...@vt.edu> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >majid hasan wrote: >> Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted >> below. Output of pdb2gmx is attached. >> > >You have numerous problems with this .pdb file: > >1. All residues are listed as being the 3' end form. Your chain should start >with a 5' end, include the "middle" residues, and end with a 3' form. > >2. 5' ends do not have phosphate on them, per force field convention. > >3. You have various incorrect atoms, and some incorrect atom names. > >Please refer to the dna.rtp file for your chosen force field to understand its >expectations. Then you will need to manually fix your .pdb file by renaming, >replacing, or removing whatever is in conflict. > >-Justin > >-- >======================================== > >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, 10 Apr 2011 18:55:15 +0800 (CST) >From: fancy2012 <fancy2...@yeah.net> >Subject: [gmx-users] probelm of using amber force field >To: gmx-users <gmx-users@gromacs.org> >Message-ID: <3ec402b.63dd.12f3f0d1e61.coremail.fancy2...@yeah.net> >Content-Type: text/plain; charset="gbk" > >Dear GMX users, > >I have a question about running MD simulation using amber force field. It is >easy to prepare the top and gro files of protein with amber force field, but >how should I prepare the itp and gro files of small molecules with GAFF force >field? I know the program ANTECHAMBER and tleap can generate the some >molecule's topology and coordinate. Could someone give me some hints? Thanks >very much in advance! > >-- > > >Best wishes, > >Qinghua Liao > >Ph.D student of Tianjin University, China >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/b7b8202b/attachment-0001.html > >------------------------------ > >Message: 5 >Date: Sun, 10 Apr 2011 07:32:13 -0400 >From: "Justin A. Lemkul" <jalem...@vt.edu> >Subject: Re: [gmx-users] probelm of using amber force field >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4da1953d.7060...@vt.edu> >Content-Type: text/plain; charset=x-gbk; format=flowed > > > >fancy2012 wrote: >> Dear GMX users, >> >> I have a question about running MD simulation using amber force >> field. It is easy to prepare the top and gro files of protein with amber >> force field, but how should I prepare the itp and gro files of small >> molecules with GAFF force field? I know the program ANTECHAMBER and >> tleap can generate the some molecule's topology and coordinate. Could >> someone give me some hints? Thanks very much in advance! > >http://code.google.com/p/acpype/ is one common approach. > >-Justin > >> >> -- >> >> _Best wishes,_ >> >> _Qinghua Liao_ >> >> _Ph.D student of Tianjin University, China_ >> > >-- >======================================== > >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, 10 Apr 2011 16:11:28 +0430 >From: mohsen ramezanpour <ramezanpour.moh...@gmail.com> >Subject: Re: [gmx-users] converging value >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <banlktimnexpd1mujgf4b9zjai4_rm_m...@mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >Dear Dr.Mark > >thank you for your attention >How long is enough? >for example I have run 200 ps for making npt(p=1 bar) for my system (300 >nm^3) >But the pressure is oscilating so much,and I can't be sure if it has >converged or not! >of course its average is approximately 5 bar (at the end of log file) > >Do you have any idea? >I know it is not any problem if a quantity is oscilating around it's >converged value. > >thanks in advance for your reply > >On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: >> >>> Dear All >>> >>> How can I determine the converged value of a simulation? >>> Because the pressure has big oscilations around it's converging value but >>> it is difficult to determine that value. >>> >> >> Longer simulations on bigger systems. >> >> Mark >> -- >> 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/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/d6cde97e/attachment-0001.html > >------------------------------ > >Message: 7 >Date: Sun, 10 Apr 2011 21:57:12 +1000 >From: Mark Abraham <mark.abra...@anu.edu.au> >Subject: Re: [gmx-users] converging value >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4da19b18.2030...@anu.edu.au> >Content-Type: text/plain; charset="iso-8859-1" > >On 10/04/2011 9:41 PM, mohsen ramezanpour wrote: >> Dear Dr.Mark >> >> thank you for your attention >> How long is enough? > >For example, when the size of error estimate reported by g_energy is >smaller than the quantity you are trying to observe. That might take >many nanoseconds in the case of observables based on fluctuations of >atomic positions. There've been lots of mailing list threads on this topic. > >Mark > >> for example I have run 200 ps for making npt(p=1 bar) for my system >> (300 nm^3) >> But the pressure is oscilating so much,and I can't be sure if it has >> converged or not! >> of course its average is approximately 5 bar (at the end of log file) >> >> Do you have any idea? >> I know it is not any problem if a quantity is oscilating around it's >> converged value. >> >> thanks in advance for your reply >> >> On Sun, Apr 10, 2011 at 3:09 PM, Mark Abraham <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>> wrote: >> >> On 10/04/2011 6:48 PM, mohsen ramezanpour wrote: >> >> Dear All >> >> How can I determine the converged value of a simulation? >> Because the pressure has big oscilations around it's >> converging value but it is difficult to determine that value. >> >> >> Longer simulations on bigger systems. >> >> Mark >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.gromacs.org/pipermail/gmx-users/attachments/20110410/ef6a449f/attachment.html > >------------------------------ > >-- >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/Support/Mailing_Lists/Search before posting! > >End of gmx-users Digest, Vol 84, Issue 81 >*****************************************
-- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists