Re: [gmx-users] how to simulate crystals in Gromacs

2011-04-07 Thread Tsjerk Wassenaar
  72  -0.082   0.795   0.592 >>     1CLC   HED2   73  -0.245   0.827   0.538 >>     1CLC   HED3   74  -0.111   0.846   0.427 >>     1CLC    H11   75  -0.949   0.960   0.123 >>     1CLC    H12   76  -0.927   0.809   0.037 >>     1CLC    H13   77  -0.799   0.929   0

Re: [gmx-users] how to simulate crystals in Gromacs

2011-04-07 Thread Mark Abraham
497 0.626 0.495 > 1CLCH3A 81 -0.754 0.495 0.531 > 1CLCHHB 82 -0.785 0.334 0.746 > 0.87600 2.58600 0.73936 0.0 0.0 0.0 0.0 > -0.41322 0.0 > > > Could you suggest some

Re: [gmx-users] how to simulate crystals in Gromacs

2011-04-06 Thread ZHANG Lu
0.334 0.746 0.87600 2.58600 0.73936 0.0 0.0 0.0 0.0 -0.41322 0.0 Could you suggest some possible reasons for the bad result of MD run? Thank you, Lu Original Message -------- Subject: Re: [gmx-users] how to simu

Re: [gmx-users] how to simulate crystals in Gromacs

2011-04-06 Thread Mark Abraham
On 7/04/2011 1:55 PM, ZHANG Lu wrote: > Dear all, >I am now trying to simulate crystals in Gromacs. >What I did was to convert the original crystal structure in cif format > to pdb format and then use genconf to replicate the cells and run MD. >Is it proper to do it in this way? It's w