[gmx-users] why gmx can not minimize the sio2?

hi all!recently,i configuratued a sio2 base!but when i minimized it in gmx,it was wrong! and show the follow messeage! --- Program mdrun, VERSION 3.3.1 Source c

[gmx-users] can gromacs simulate the c60?

hi everyone I am planning to simulated the C60 ,but i am not sure whether the gromacs can simulate it ! I have read a particle that simulated the CNT by using the gromacs and using the Morse potential!so i want to know is it correct to C60?if right,how to get the morse parameters? thanks

[gmx-users] about afm !

hi all in my model ,in order to simulate a LB monolayer adsorb on base ,the monolayer composed of 108 c17cooh that in a plane ! i need to pull the monolayer!how can i to pull the monolayer along the z direction while keep the molecular in a plane ！ __

[gmx-users] afm does not work!

hi everyone I need to pull the two parallel monolayers together,the two monolayers are in the x-y plane , so i pull the one along the z direction,but it stay still! i tried several times ,but all failed! i use the [position_restraints ] 　　 1 1 9000

[gmx-users] how to add a force field or potential fu nction?

hi all ! recently ,i want to add C60 in my monolayer system ,but i do not know how to add the C60 potential function ? and i also want to know how to add a force field! could anyone help me? thanks! ___ gmx-users mailing listgmx-users@grom

[gmx-users] L-BFGS energy minimization wrong!

hi everyone !    i have ask some questions about energy minimization before ,but still,there are problems !this time it show: --- Program mdrun, VERSION 3.3.1    Source code file: nsg

[gmx-users] do the non-bong ennergy influence the opt imization?

hi all     as i use the l-bfgs to optimize my system ,which composed of two monolayers that each contain 36 CH3(CH2)14COOH molecules ,when the distance bettwen the two monolayes is 1.5nm,the minimization go smoothly,but when  decrease to 1.2nm,the monilayers turn over(A-B:B-A TO B-A:A-B,A B are  th

[gmx-users] wrong optimization result!!!

hi all     my system haa two monolayers ,when i set the two 1.5nm apart each other ,it can optimize  smoothly,but the two monolayers turn over when 1.2nm?and show segementation fault(core dump),anyone can help me? thanks !  ___ gmx-users mailing listg

[gmx-users] how to calculate the shear force(ii)

hi   i didn't say in ditailly about my question in last mail .now i write it again:    my system is composed of two monolayers,i keep one still and pull the other one ,and i need to calculated the shear force bettwen them,and the friction force! but i just have the edr file ,no other file,could i

[gmx-users] how to calculate the shear force in gmx

hi all user i want to calculate the shear force ,but no way! i found 9 pre items in .edr file !what is it used to do ?how can i use it? any one can give some advise ?   thanks!        ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

[gmx-users] can i control the solvent box size?

hello everyone     i want to know can i change or control the solvent size:my system is composed of two monolayers,and i want to add solvent just bettwen the monolayers! can anyone help me ?thanks addvaced!         美 女 恐 怖 败 家 秀 ( 组 图 ) 独 家 披 露 ! 小 资 女 人 8 个 绝 顶 隐 秘 的 趣 事 ( 组 图 ) __

[gmx-users] about pulling

everyone i want to do the afm on my system,i want to pull one of my two monolayers and keep the other  one still,i only have a pull.ppa as input file,but it show input/output error pull.ndx! does that for no pull.ndx file?    anyone can tell me how to do afm? thanks advanced!         3G 时 代

[gmx-users] energy minimization end too early!

hi everyone     today ,I do minimization with my system,my system with two face to face monolayers composed of ch3(ch2)13cooh, when i set the molecular as CHO group,it pass smoothly,because i want to pull the upper layer ,so  i set the upper layer group DHO that has the same parameters with CHO itp

[gmx-users] about box size (III)

hi everyone    since i met the problem several days ago,mang good friends help me !i thank them very much!   and now,i explicit my problem  and the solution ditailly,hope to help who will meet the same problem!    my system is composed of two opesite monolayers,and the size is 3,2,6 in x,y ,z direc

[gmx-users] about box size (II)

thanks chris.neale!  when i change  the size to 6.0 (my  system is 3,2,6) ,the upper monolayer turn around ,the bottom to the top ,top to  the bottom ,is it the too big size in the x and y direction? should i to enlarge my sysytem to (6,6,6) to suit the box size?   thanks!       3G 时 代 来 临 了，坚 决

[gmx-users] about box size

hi everyone     my system contain 2 monolayers,and it is more then 6nm in the z direction,and my box is 3.000,3.000,3.000, so it always wrong when mdrun,it said the box only this size,i want to know how to resolve my quetion ? 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

[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 ！

[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 t

[gmx-users] about equilibration and minimization!

i have conformed my system well,then i used the l-bfgs to minimize it for 5000 steps,but it stopped at 245th steps,for system han no change,then ,i used steep but no used,it show "Too many LINCS warnings (10997) - aborting to avoid logfile runaway.   

[gmx-users] mdp wrong

  hi   follow the last problem ,i checked my gro,itp and modifid,but this time ,"invalid command line argument",what's that mean? is still my mdp'wrong?but this mdp that i test well in other gro ,and itp in ffgrom96,and this time ,my forcefield is ffoplsaa,is there any different in the mdp? 3G 时

[gmx-users] is it my mdp's wrong?

hi all     my system is lb film of 36 c14cooh long chains! my gro and itp wrote correctly,but when i used the l-bfgs to minimize the system ,the grompp show invalid order "moleculetype",when use the MD ,it showed the atom number in gro not the same as in itp?    is it my mdp's wrong?   3G 时 代 来 临

[gmx-users] does the conformation cause this error?

hi all i have a problem:when i did the mdrun ,it stopped early for error:Maximum force =  9.0996275e+09 on atom 606 Norm of force =  2.8519283e+08    does this cause by the conformation?and how to resolve it?     3G 时 代 来 临 了，坚 决

[gmx-users] how to write a annealing .mdp

hello everyone   i want to anneal my system,but i don't konw how to wrote a right annealing-mdp! could anyone give me a moldel?   tanks in advaced!               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] can the GMX model the monolayer frict ion ?

  hello everyone     I want to know whether GMX can simulate the LB monolayer  or selfassemble monolayer on base ?if can not ,could advise one to me?   thanks!      买 这 些 让 女 友 很 兴 奋 ( 图 ) 真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性 生 活 ( 组 图 ) ___

[gmx-users] why the mdrun stop

  hello ,everyone   I have two problems: (1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and use the frocefiled of ffgmx, but the mdrun can only going to the 2th step,and the some chains change large (2)can this program do the nanotribology of   monolayer? thanks advanced! wait for you