You can change integrator back to l-bfgs and the requested atoms will be non-movable as well. MD in the file is just because I ran EM first and then MD to check the problem. So, the last keyword is present.
What kind of calculation do you want to perform at all? - It's even better to run MD for some time to relax the system completely. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 Hi > > > > I performed EM with all your input files and got the same results as you > did(Gromacs-3.3.3). The C and O in carbonyl groups are nonmovable. The only > difference between your > > > > and my mdp file is the "intergrator". It is "md" in yours and "l-bfgs" in > mine. In Groamcs manual, "1-bfg" method is used for EM. I want to know > whether "md" can be used for > > > > EM. I will perform EM in Gromacs-4.0.5 lately. > > > > Thank you for your time and patience! > > > > ; RUN CONTROL PARAMETERS > integrator = md > ; Start time and timestep in ps > tinit = 0 > dt = 0.002 > nsteps = 2000 > ; For exact run continuation or redoing part of a run > init_step = 0 > ; mode for center of mass motion removal > comm-mode = Linear > ; number of steps for center of mass motion removal > nstcomm = 1 > ; group(s) for center of mass motion removal > comm-grps = > > > ----- 原始邮件 ----- > 发件人：Vitaly V. Chaban <vvcha...@gmail.com> > 收件人：toby10222...@sina.com, gmx-users@gromacs.org > 主题：Re: 回复：Re: 回复：Re: How to freeze the atoms? > 日期：2009-7-4 17:13:43 > > > Hi, > > First of all I suggest you to upgrade to the current version. > > In the next email I also attach all the files I used for a test run of your > system. > > ~Vitaly > > > 2009/7/4 <toby10222...@sina.com> > >> Gromacs 3.3.3, there is no warning when I use shake with EM. >> ----- 原始邮件 ----- >> 发件人：Vitaly V. Chaban <vvcha...@gmail.com> >> 收件人：toby10222...@sina.com, gmx-users@gromacs.org >> 主题：Re: 回复：Re: How to freeze the atoms? >> 日期：2009-7-4 13:47:47 >> >> >> What gromacs version do you use for now? The new version should warn you >> that shake is impossible with EM. >> >> ~ Vitaly >> >> >>
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