Re: [gmx-users] bond lost (II)
zzhwise1 wrote: > about the second question,is that ,when i use the md as integrator,the > feedback show the atomnumber of gro was not the same as top which show 0 > atom? but when i use the l-bfgs as integrator, there was no wrong,and > goes smoothly! > and i never know why! Neither will we know, unless you can do as I suggested last time - "You need to describe the problem fully, include contents of small files where appropriate, and quote the feedback you get from the gromacs tools." Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bond lost (II)
about the second question,is that ,when i use the md as integrator,the feedback show the atomnumber of gro was not the same as top which show 0 atom? but when i use the l-bfgs as integrator, there was no wrong,and goes smoothly! and i never know why! 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bond lost!
zzhwise1 wrote: > good everyone >i have 2 questions : > 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for > 5000steps,but it stopped at 467th step,and i found the conformation > break,8chains'lost the C-OH bonds,why there was this and what cause > this?was this the wrong itp or mdp? Your topology was not correct. Compare the contents of the .top file with the .itp file it was sourced from. > 2) when i change the mdp with md,then show the gro atomnumber not > incorred with top?why?i still could not find out the reason! I can't understand this. You need to describe the problem fully, include contents of small files where appropriate, and quote the feedback you get from the gromacs tools. Or you could employ a mind-reader. I know what's cheaper :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bond lost!
good everyone i have 2 questions : 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for 5000steps,but it stopped at 467th step,and i found the conformation break,8chains'lost the C-OH bonds,why there was this and what cause this?was this the wrong itp or mdp? 2) when i change the mdp with md,then show the gro atomnumber not incorred with top?why?i still could not find out the reason! can anyone help me? thankS! 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
