[gmx-users] how to simulate crystals in Gromacs
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Apr 7 10:54:31 CEST 2011
Hi,
When building crystals, you first have to generate all symmetry mates
for a single unit cell. This may involve both rotations and
translations, and the information should be present in the structure
file. The unit cell can then be used to build a larger crystal with
genconf. With Pymol you can build symmetry mates from a structure
file, and on the pymolwiki there's a script to build a unit cell for a
given structure.
Mind first to convert the structure into the proper format for the
force field description you're using, as it will be more convenient to
build the topology for the crystal afterwards.
Hope it helps,
Tsjerk
2011/4/7 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
More information about the gromacs.org_gmx-users
mailing list