[gmx-users] how to simulate crystals in Gromacs
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Apr 7 09:25:19 CEST 2011
On 7/04/2011 4:21 PM, ZHANG Lu wrote:
> 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?
I don't know. When you opened it in a visualization program and saw the
periodic box, and turned on the "show periodic images" option, did it
look reasonable?
Mark
> 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.Abraham at anu.edu.au>
> Date: Thu, April 7, 2011 12:05 pm
> To: "Discussion list for GROMACS users" <gmx-users at 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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