Gmx-users-request，您好！ 您在 2010年10月9日，18:54:33 写道:
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Re: how to write a rtp file for amido amine (Mark Abraham) > ---------------------------------------------------------------------- > Message: 1 > Date: Sat, 9 Oct 2010 14:40:02 +0400 > From: ???? ????? <magistrpet...@gmail.com> > Subject: [gmx-users] output force > To: gmx-users@gromacs.org > Message-ID: > <aanlktinum8y=m9dbpjkvh5pmr_zuk_k3uec81cyub...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > Hello dear gmx-users! > When calculated forces in gromacs to produce pmf, we have the net force in > output. For example: > ... > # > # Giving Russians Opium May Alter Current Situation > # > @ title "Pull force" > @ xaxis label "Time (ps)" > @ yaxis label "Force (kJ/mol/nm)" > @TYPE xy > 0.000000 1017490.761270 > 0.002000 -253098.034916 > 0.004000 -43856.400160 > 0.006000 48980.619113 > 0.008000 52103.053067 > 0.010000 33788.090031 > 0.012000 19096.388350 > 0.014000 14094.738810 > 0.016000 14027.621966 > 0.018000 15162.993741 > 0.020000 14136.978177 > ... etc. > What sould I do to get the net force of protein-solvent interactions or > protein-protein interactions or solvent-solvent interactions instead and get > output .xvg file in the form like this: > time Force(type1) Force(type2) Force(type3) > t1 f1 f1 f1 > t2 f2 f2 f2 > t3 f3 f3 f3 > ... ... ... ... > etc. > Thank you for attention and I hope you will help me! > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20101009/1b8ec190/attachment-0001.html > ------------------------------ > Message: 2 > Date: Sat, 09 Oct 2010 21:50:10 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] output force > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <fbe6fea12e6a6.4cb0e...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-5" > You can get that with cunning use of energy groups and mdrun -rerun, but not > mid-simulation. > Mark > ----- Original Message ----- > From: 空忄 哭咿?<magistrpet...@gmail.com> > Date: Saturday, October 9, 2010 21:41 > Subject: [gmx-users] output force > To: gmx-users@gromacs.org >> Hello dear gmx-users! >> >> When calculated forces in gromacs to produce pmf, we have the net force in >> output. For example: >> ... >> # >> # Giving Russians Opium May Alter Current Situation >> # >> @ title "Pull force" >> @ xaxis label "Time (ps)" >> @ yaxis label "Force (kJ/mol/nm)" >> @TYPE xy >> 0.000000 1017490.761270 >> 0.002000 -253098.034916 >> 0.004000 -43856.400160 >> 0.006000 48980.619113 >> 0.008000 52103.053067 >> 0.010000 33788.090031 >> 0.012000 19096.388350 >> 0.014000 14094.738810 >> 0.016000 14027.621966 >> 0.018000 15162.993741 >> 0.020000 14136.978177 >> ... etc. >> >> What sould I do to get the net force of protein-solvent interactions or >> protein-protein interactions or solvent-solvent interactions instead and get >> output .xvg file in the form like this: >> >> time Force(type1) Force(type2) Force(type3) >> >> t1 f1 f1 f1 >> t2 f2 f2 f2 >> t3 f3 f3 f3 >> ... ... ... ... >> etc. >> >> Thank you for attention and I hope you will help me! >> -- >> 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/20101009/6027dfd5/attachment-0001.html > ------------------------------ > Message: 3 > Date: Sat, 09 Oct 2010 21:53:41 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] how to write a rtp file for amido amine > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <fbdb87472f446.4cb0e...@anu.edu.au> > Content-Type: text/plain; charset="us-ascii" > ----- Original Message ----- > From: lammps lammps <lammp2fo...@gmail.com> > Date: Saturday, October 9, 2010 19:27 > Subject: [gmx-users] how to write a rtp file for amido amine > To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Hi everybody, >> >> I want to use pdb2gmx command to create a .gro file and a .top file for >> PAMAM whose repeat unit is amidoamine ( attached ). >> >> / >> ---CH2--CH2--CO-NH-CH2-CH2-N (see the attached figure) >> \ >> >> The atom N have two same branches with --CH2--. I write the rtp file for it >> as follows: >> >> [ atoms ] >> C1 opls_245 -0.050 1 >> ......... >> [ bonds ] >> C1 -N7 >> ....... >> C6 N7 >> N7 +C1> N7 +C1 >> >> It seems not work, which gives a wrong top structure. The question is how >> can I deal with the two branches of N. Any suggestion is appreciated. > pdb2gmx is intended only for work with linear heteropolymers. Any > more complex things (e.g. disulfides, branched structures) have to > be engineered using the specbonds.dat mechanism. > Mark > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20101009/0c376d18/attachment.html > ------------------------------ -- 此致 敬礼！ tjmu mailto:tjmu_hac...@yahoo.com.cn __________________________________________________ �Ͽ�ע���Ż�����������������? http://cn.mail.yahoo.com -- 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
