Thank you for your answer.
Could you give me some advice on the size of cell box? What is the proper
size if I want to do MD simulation in crystal environment?
I didn't change the cell size when I convert cif file to pdb file; in
other word, I didn't use editconf to produce the cell box. What I did was
just :
pdb2gmx -> genconf ( -nbox 10 10 10 -dist 0.5 0.5 0.5 ) -> genbox. Was it
wrong?
Below is the coordination and cell box after I run pdb2gmx. I use water to
fill in the box after genconf.
1CLC OBD 1 -0.042 0.476 0.219
1CLC O1D 2 -0.298 0.731 0.310
1CLC O2D 3 -0.163 0.650 0.469
1CLC O1A 4 -0.697 0.691 0.093
1CLC O2A 5 -0.822 0.826 0.214
1CLC CMB 6 -0.877 0.164 0.937
1CLC CAB 7 -0.708 -0.089 1.050
1CLC CBB 8 -0.820 -0.108 1.104
1CLC CMC 9 -0.224 -0.302 0.948
1CLC CAC 10 0.016 -0.236 0.743
1CLC CBC 11 0.014 -0.333 0.627
1CLC CMD 12 0.106 0.164 0.377
1CLC CAD 13 -0.122 0.426 0.298
1CLC CBD 14 -0.260 0.494 0.322
1CLC CAA 15 -0.598 0.558 0.332
1CLC CBA 16 -0.685 0.684 0.330
1CLC CMA 17 -0.672 0.604 0.686
1CLC CGD 18 -0.246 0.640 0.366
1CLC CED 19 -0.149 0.789 0.509
1CLC CGA 20 -0.733 0.732 0.198
1CLC C1 21 -0.878 0.885 0.095
1CLC CMG 22 -0.373 0.175 0.683
1CLC NB 23 -0.540 0.110 0.783
1CLC NC 24 -0.278 -0.005 0.729
1CLC ND 25 -0.234 0.194 0.534
1CLC NA 26 -0.492 0.328 0.583
1CLC C1B 27 -0.657 0.181 0.798
1CLC C2B 28 -0.741 0.114 0.897
1CLC C3B 29 -0.670 0.008 0.944
1CLC C4B 30 -0.543 0.006 0.871
1CLC CHC 31 -0.442 -0.086 0.890
1CLC C1C 32 -0.317 -0.091 0.824
1CLC C2C 33 -0.214 -0.193 0.847
1CLC C3C 34 -0.112 -0.163 0.760
1CLC C4C 35 -0.154 -0.045 0.688
1CLC CHD 36 -0.078 0.019 0.591
1CLC C1D 37 -0.112 0.131 0.520
1CLC C2D 38 -0.033 0.201 0.421
1CLC C3D 39 -0.115 0.309 0.380
1CLC C4D 40 -0.234 0.301 0.455
1CLC CHA 41 -0.325 0.405 0.430
1CLC C1A 42 -0.448 0.417 0.491
1CLC C2A 43 -0.545 0.533 0.476
1CLC C3A 44 -0.657 0.499 0.577
1CLC C4A 45 -0.612 0.366 0.634
1CLC CHB 46 -0.687 0.294 0.727
1CLC HMB1 47 -0.919 0.099 1.010
1CLC HMB2 48 -0.868 0.263 0.978
1CLC HMB3 49 -0.941 0.167 0.851
1CLC HAB 50 -0.629 -0.151 1.086
1CLC HBB1 51 -0.831 -0.182 1.180
1CLC HBB2 52 -0.905 -0.049 1.074
1CLC HMC1 53 -0.317 -0.294 1.000
1CLC HMC2 54 -0.143 -0.294 1.018
1CLC HMC3 55 -0.219 -0.397 0.899
1CLC HAC1 56 0.029 -0.295 0.831
1CLC HAC2 57 0.089 -0.162 0.718
1CLC HBC1 58 0.108 -0.382 0.619
1CLC HBC2 59 -0.063 -0.406 0.643
1CLC HBC3 60 -0.006 -0.280 0.536
1CLC HMD1 61 0.139 0.078 0.430
1CLC HMD2 62 0.172 0.246 0.397
1CLC HMD3 63 0.106 0.144 0.272
1CLC HBD 64 -0.320 0.500 0.234
1CLC HAA1 65 -0.661 0.476 0.307
1CLC HAA2 66 -0.512 0.580 0.271
1CLC HBA1 67 -0.774 0.656 0.383
1CLC HBA2 68 -0.622 0.762 0.367
1CLC HMA1 69 -0.751 0.575 0.753
1CLC HMA2 70 -0.580 0.612 0.740
1CLC HMA3 71 -0.696 0.698 0.642
1CLC HED1 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 0.037
1CLC HHC 78 -0.460 -0.161 0.963
1CLC HHD 79 0.018 -0.024 0.570
1CLC H2A 80 -0.497 0.626 0.495
1CLC H3A 81 -0.754 0.495 0.531
1CLC HHB 82 -0.785 0.334 0.746
0.87600 2.58600 0.73936 0.00000 0.00000 0.00000 0.00000
-0.41322 0.00000
Could you suggest some possible reasons for the bad result of MD run?
Thank you,
Lu
---------------------------- Original Message ----------------------------
Subject: Re: [gmx-users] how to simulate crystals in Gromacs
From: "Mark Abraham" <mark.abra...@anu.edu.au>
Date: Thu, April 7, 2011 12:05 pm
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
--------------------------------------------------------------------------
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 workable. Whether you need to replicate depends on the size of the
periodic cell. Whether your box had enough space around the "outer"
atoms is also a concern.
> Because the structure I got after MD
> run was completely a mess ( not like crystals any more).
> Could anyone tell me the correct way to do MD simulation in crystal
> environment?
There are a large number of possible reasons of the problem. We simply
do not have enough information to suggest anything.
Mark
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