Re: [gmx-users] The molecule size

2006-09-17 Thread 主月 ：）
> Hi:>  > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition .>  > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to acce

Re: [gmx-users] bond lost (II)

2006-09-17 Thread Mark Abraham
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

[gmx-users] bond lost (II)

2006-09-17 Thread zzhwise1
 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 ！

Re: [gmx-users] The molecule size

2006-09-17 Thread Mark Abraham
主月 ：） wrote: > Hi: > > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition . > > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to

Re: [gmx-users] bond-bond and bond-angle cross terms

2006-09-17 Thread Mark Abraham
Camilo Calderon wrote: Hi all! I am new to the GROMACS-world, and I am mystified. How do I implement the 3 body potentials advertised in sec. 4.2.8 and sec. 4.2.9 of the GROMACS 3.3 manual? Right now I have the following: [ cross_cross_bond ] ;ai aj funct r1e r2e krr [ cross_bond_angl

Re: [gmx-users] Re: Using ACE and NAC with oplsaa

2006-09-17 Thread Mark Abraham
[EMAIL PROTECTED] wrote: Appologies, two entries are required (the first is for ACE and the second is for NAC): [ dihedraltypes ] ; ijkl func coefficients CT C N CT_23 30.28798 -4.81160 -25.47638 0.0 0.0 0.0 For ACE (Sept2006) ad

[gmx-users] The molecule size

2006-09-17 Thread 主月 ：）
Hi:   Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition .   The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as foll

Re: [gmx-users] bond lost!

2006-09-17 Thread Mark Abraham
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

[gmx-users] bond lost!

2006-09-17 Thread zzhwise1
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

Re: [gmx-users] openmpi

2006-09-17 Thread gigo
Hi, I'm using openmpi on our 24-nodes 2 cores each cluster without any problem so far. I run my jobs under torque and I did not change any of default settings. With my system it scales rather well on 4 nodes, but I have no problems with running more. Grzegorz Wieczorek Department of Bioinfor