[gmx-users] spectral density calculation with GROMACS

2011-03-09 Thread ZHANG Lu 
Dear all,
   I am now developing a set of force field parameters and I want to
calculate the spectral density with the normal mode analysis in GROMACS
to check my parameters.
   The point here is that I want to get a plot (spectral density VS
frequencies). Could anybody give me some slides or tutorials so that I
can follow it?
   Thank you in advance.

Best,
Lu

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[gmx-users] how to simulate crystals in Gromacs

2011-04-06 Thread ZHANG Lu 
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? 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?
   Many thanks.

Best,
Lu

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

2011-04-06 Thread ZHANG Lu 
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.

1CLCOBD1  -0.042   0.476   0.219
1CLCO1D2  -0.298   0.731   0.310
1CLCO2D3  -0.163   0.650   0.469
1CLCO1A4  -0.697   0.691   0.093
1CLCO2A5  -0.822   0.826   0.214
1CLCCMB6  -0.877   0.164   0.937
1CLCCAB7  -0.708  -0.089   1.050
1CLCCBB8  -0.820  -0.108   1.104
1CLCCMC9  -0.224  -0.302   0.948
1CLCCAC   10   0.016  -0.236   0.743
1CLCCBC   11   0.014  -0.333   0.627
1CLCCMD   12   0.106   0.164   0.377
1CLCCAD   13  -0.122   0.426   0.298
1CLCCBD   14  -0.260   0.494   0.322
1CLCCAA   15  -0.598   0.558   0.332
1CLCCBA   16  -0.685   0.684   0.330
1CLCCMA   17  -0.672   0.604   0.686
1CLCCGD   18  -0.246   0.640   0.366
1CLCCED   19  -0.149   0.789   0.509
1CLCCGA   20  -0.733   0.732   0.198
1CLC C1   21  -0.878   0.885   0.095
1CLCCMG   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
1CLCC1B   27  -0.657   0.181   0.798
1CLCC2B   28  -0.741   0.114   0.897
1CLCC3B   29  -0.670   0.008   0.944
1CLCC4B   30  -0.543   0.006   0.871
1CLCCHC   31  -0.442  -0.086   0.890
1CLCC1C   32  -0.317  -0.091   0.824
1CLCC2C   33  -0.214  -0.193   0.847
1CLCC3C   34  -0.112  -0.163   0.760
1CLCC4C   35  -0.154  -0.045   0.688
1CLCCHD   36  -0.078   0.019   0.591
1CLCC1D   37  -0.112   0.131   0.520
1CLCC2D   38  -0.033   0.201   0.421
1CLCC3D   39  -0.115   0.309   0.380
1CLCC4D   40  -0.234   0.301   0.455
1CLCCHA   41  -0.325   0.405   0.430
1CLCC1A   42  -0.448   0.417   0.491
1CLCC2A   43  -0.545   0.533   0.476
1CLCC3A   44  -0.657   0.499   0.577
1CLCC4A   45  -0.612   0.366   0.634
1CLCCHB   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
1CLCHAB   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
1CLCHBD   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
1CLCH11   75  -0.949   0.960   0.123
1CLCH12   76  -0.927   0.809   0.037
1CLCH13   77  -0.799   0.929   0.037
1CLCHHC   78  -0.460  -0.161   0.963
1CLCHHD   79   0.018  -0.024   0.570
1CLCH2A   80  -0.497   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 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" 
Date:Thu, April 7, 2011 12:05 pm
To:  "Discussion list for GROMACS users" 
------

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.
>

[gmx-users] A Force Field Paper including Heme Proteins

2012-07-31 Thread ZHANG Lu 
Dear gromacs users,
  We just published a paper titled "Force field development for cofactors
in the photosystem II" in Journal of Computational Chemistry, which
includes the Amber03 compatible force field for heme-B and works well
with heme proteins. You may use it for reference at your convenience.
  The link for the paper is http://www.ncbi.nlm.nih.gov/pubmed/22685077

Best,
Lu

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[gmx-users] proper dihedral types in the topology

2011-08-27 Thread ZHANG Lu 
Dear man or madam,
   I have a question about the dihedral types in the topology.
   If I made the topology by hand, is it possible to combine the type 9
and type 3 for proper dihedrals? Any comment about that?
   Thanks.

Best,
Lu

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