[gmx-users] Hydroxyapatite MD odd behavior
Justin Lemkul
jalemkul at vt.edu
Mon Aug 6 19:52:46 CEST 2012
On 8/6/12 1:35 PM, Ramon Garduno wrote:
> Justin,
>
> Of course you are right, for troubleshooting the smaller, the better. However,
> in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell,
> the later is by no means small.
>
> In response to your comments, I will appreciate very much if you could examine
> the PDB files related to the HAP geometry. They can be downloaded from
> http://www.fis.unam.mx/~ramon/CursoDF/HAP/ They are named hap-2 and slab-2,
> the first one corresponds to the unit cell from which we built the
> slab (which is labed slab-2) upon which we want to study the peptide
> interactions. The *.itp file I sent before corresponds to hap-2.
>
> We hope that with this information you can help us in detecting the source of
> the problem that has bother us for some time now...
>
Please provide all the necessary files, including topologies and modified force
field files. I don't have time to make and double-check all of these files and
it's better to use exactly the same files you've been trying to use.
> Sorry for the delay in responding but I had problems sending the pdb files
> through gmx-users...
>
Attachments are no longer allowed due to recent viruses and spam. Posting files
for download from external sites is the only way to provide files (aside from
copying and pasting their contents, but external download is probably easiest in
many cases).
-Justin
> Cheers,
>
> On Fri, 27 Jul 2012 22:29:31 -0400, Justin Lemkul wrote
>> On 7/27/12 8:54 PM, Ramon Garduno wrote:
>>> Dear Justin,
>>>
>>> Thanks for your quick reply. Actually, we think that the topology is OK,
>>> however HAP's parameters could be wrong, we are checking on this...
>>>
>>
>> I would say that the topology being OK and the parameters being
>> wrong are contradictory statements ;)
>>
>>> These are the topology files used for HAP. The names associated to the atoms
>>> present on the slab are:
>>>
>>
>> Can you reduce the system to just one molecule? It appears there
>> are several molecules in the .itp below and it's quite hard to keep
>> track of everything without seeing the corresponding coordinate file
>> as well. A single molecule would be a lot easier to deal with, and
>> a coordinate file would allow for better troubleshooting (the
>> smaller, the better).
>>
>> -Justin
>>
>>> ACa - Ca2+
>>> AP - P
>>> AO1 - O(P)
>>> AO4 - O(H)
>>> AH - H
>>>
>>> 1- ffnonbonded.itp
>>> [ atomtypes ]
>>> ;name at.num mass charge ptype c6 c12
>>> ACa 40.0800 0.000 A 7.34375e-05 4.755341e-08
>>> AP 30.9738 0.000 A 1.6701174e-03 2.9953696e-06
>>> AO1 15.9994 0.000 A 1.8737825e-04 1.4573462e-07
>>> AO4 15.9994 0.000 A 9.793663e-05 8.5730467e-08
>>> AH 1.00800 0.000 A 7.17e-11 5.497e-16
>>>
>>> [ nonbond_params ]
>>> ; i j func c6 c12
>>> ACa ACa 1 7.34375e-05 4.755341e-08
>>> ACa AO4 1 8.480696e-05 6.38496e-08
>>> ACa AH 1 7.2564e-08 5.112734e-12
>>> ACa AO1 1 1.173055e-04 8.324769e-08
>>> ACa AP 1 3.50213e-04 3.77223e-07
>>> AO4 AO4 1 1.8737825e-04 8.5730467e-08
>>> AO4 AH 1 8.37977e-08 6.864841e-12
>>> AO4 AO1 1 1.354666e-04 1.117761e-07
>>> AO4 AP 1 1.2789279e-03 5.0674888e-07
>>> AH AH 1 7.17e-11 5.497e-16
>>> AH AO1 1 1.159095e-07 8.950437e-12
>>> AH AP 1 3.460454e-07 4.057776e-11
>>> AO1 AO1 1 1.8737825e-04 1.4573462e-07
>>> AO1 AP 1 5.594137e-04 6.607035e-07
>>> AP AP 1 1.6701174e-03 2.9953696e-06
>>>
>>> 2- HAP-MODEL4-100.itp
>>> ;; topology file for a HAP, created by Eduardo Villarreal & Ramon Garduno
>>> ;; from hap.itp taken from diferente papers
>>> ;; one can use Gromacs force-field files (ffgmx*.itp)
>>> ;; If you use this topology file, please cite to Eduardo Villarreal & Ramon
>>> Garduno
>>> ;;
>>>
>>> [ moleculetype ]
>>> ; Name nrexcl
>>> HAP 3
>>>
>>> [ atoms ]
>>> ;aqui se hace coincidir cada atomo en la celda de unidad
>>> ; id atype resnr resane aname cgnr charge mass
>>> 1 AO1 1 HAP O3A 1 -1.4000 15.9994
>>> 2 AO1 1 HAP O3B 2 -1.4000 15.9994
>>> 3 AO1 1 HAP O3C 3 -1.4000 15.9994
>>> 4 AO1 1 HAP O3D 4 -1.4000 15.9994
>>> 5 AO1 1 HAP O3E 5 -1.4000 15.9994
>>> 6 AO1 1 HAP O3F 6 -1.4000 15.9994
>>> 7 AO1 1 HAP O3G 7 -1.4000 15.9994
>>> 8 AO1 1 HAP O3H 8 -1.4000 15.9994
>>> 9 AO1 1 HAP O3I 9 -1.4000 15.9994
>>> 10 AO1 1 HAP O3J 10 -1.4000 15.9994
>>> 11 AO1 1 HAP O3K 11 -1.4000 15.9994
>>> 12 AO1 1 HAP O3L 12 -1.4000 15.9994
>>> 13 AO1 1 HAP O3M 7 -1.4000 15.9994
>>> 14 AO1 1 HAP O3N 8 -1.4000 15.9994
>>> 15 AO1 1 HAP O3O 9 -1.4000 15.9994
>>> 16 AO1 1 HAP O3P 10 -1.4000 15.9994
>>> 17 AO1 1 HAP O3Q 11 -1.4000 15.9994
>>> 18 AO1 1 HAP O3R 12 -1.4000 15.9994
>>> 19 AO1 1 HAP O3S 1 -1.4000 15.9994
>>> 20 AO1 1 HAP O3T 2 -1.4000 15.9994
>>> 21 AO1 1 HAP O3U 3 -1.4000 15.9994
>>> 22 AO1 1 HAP O3V 4 -1.4000 15.9994
>>> 23 AO1 1 HAP O3W 5 -1.4000 15.9994
>>> 24 AO1 1 HAP O3X 6 -1.4000 15.9994
>>> 25 AO1 1 HAP O1A 1 -1.4000 15.9994
>>> 26 AO1 1 HAP O1B 2 -1.4000 15.9994
>>> 27 AO1 1 HAP O2A 1 -1.4000 15.9994
>>> 28 AO1 1 HAP O2B 2 -1.4000 15.9994
>>> 29 AP 1 HAP P1A 1 2.6000 30.9738
>>> 30 AP 1 HAP P1B 2 2.6000 30.9738
>>> 31 ACa 1 HAP CaA 17 2.0000 40.0800
>>> 32 ACa 1 HAP CaB 18 2.0000 40.0800
>>> 33 AO1 1 HAP O1C 3 -1.4000 15.9994
>>> 34 AO1 1 HAP O1D 4 -1.4000 15.9994
>>> 35 AO1 1 HAP O2C 3 -1.4000 15.9994
>>> 36 AO1 1 HAP O2D 4 -1.4000 15.9994
>>> 37 AP 1 HAP P1C 3 2.6000 30.9738
>>> 38 AP 1 HAP P1D 4 2.6000 30.9738
>>> 39 ACa 1 HAP CaC 19 2.0000 40.0800
>>> 40 ACa 1 HAP CaD 20 2.0000 40.0800
>>> 41 AO1 1 HAP O1E 5 -1.4000 15.9994
>>> 42 AO1 1 HAP O1F 6 -1.4000 15.9994
>>> 43 AO1 1 HAP O2E 5 -1.4000 15.9994
>>> 44 AO1 1 HAP O2F 6 -1.4000 15.9994
>>> 45 AP 1 HAP P1E 5 2.6000 30.9738
>>> 46 AP 1 HAP P1F 6 2.6000 30.9738
>>> 47 ACa 1 HAP CaE 21 2.0000 40.0800
>>> 48 ACa 1 HAP CaF 22 2.0000 40.0800
>>> 49 AO1 1 HAP O1G 7 -1.4000 15.9994
>>> 50 AO1 1 HAP O1H 8 -1.4000 15.9994
>>> 51 AO1 1 HAP O2G 7 -1.4000 15.9994
>>> 52 AO1 1 HAP O2H 8 -1.4000 15.9994
>>> 53 AP 1 HAP P1G 7 2.6000 30.9738
>>> 54 AP 1 HAP P1H 8 2.6000 30.9738
>>> 55 ACa 1 HAP CaG 23 2.0000 40.0800
>>> 56 ACa 1 HAP CaH 24 2.0000 40.0800
>>> 57 AO1 1 HAP O1I 9 -1.4000 15.9994
>>> 58 AO1 1 HAP O1J 10 -1.4000 15.9994
>>> 59 AO1 1 HAP O2I 9 -1.4000 15.9994
>>> 60 AO1 1 HAP O2J 10 -1.4000 15.9994
>>> 61 AP 1 HAP P1I 9 2.6000 30.9738
>>> 62 AP 1 HAP P1J 10 2.6000 30.9738
>>> 63 ACa 1 HAP CaI 25 2.0000 40.0800
>>> 64 ACa 1 HAP CaJ 26 2.0000 40.0800
>>> 65 AO1 1 HAP O1K 11 -1.4000 15.9994
>>> 66 AO1 1 HAP O1L 12 -1.4000 15.9994
>>> 67 AO1 1 HAP O2K 11 -1.4000 15.9994
>>> 68 AO1 1 HAP O2L 12 -1.4000 15.9994
>>> 69 AP 1 HAP P1K 11 2.6000 30.9738
>>> 70 AP 1 HAP P1L 12 2.6000 30.9738
>>> 71 ACa 1 HAP CaK 27 2.0000 40.0800
>>> 72 ACa 1 HAP CaL 28 2.0000 40.0800
>>> 73 ACa 1 HAP CaM 29 2.0000 40.0800
>>> 74 ACa 1 HAP CaN 30 2.0000 40.0800
>>> 75 ACa 1 HAP CaO 31 2.0000 40.0800
>>> 76 ACa 1 HAP CaP 32 2.0000 40.0800
>>> 77 ACa 1 HAP CaQ 33 2.0000 40.0800
>>> 78 ACa 1 HAP CaR 34 2.0000 40.0800
>>> 79 ACa 1 HAP CaS 35 2.0000 40.0800
>>> 80 ACa 1 HAP CaT 36 2.0000 40.0800
>>> 81 AO4 1 HAP O4A 13 -1.6000 15.9994
>>> 82 AO4 1 HAP O4B 14 -1.6000 15.9994
>>> 83 AH 1 HAP H1A 13 0.6000 1.00800
>>> 84 AH 1 HAP H1B 14 0.6000 1.00800
>>> 85 AO4 1 HAP O4C 15 -1.6000 15.9994
>>> 86 AO4 1 HAP O4D 16 -1.6000 15.9994
>>> 87 AH 1 HAP H1C 15 0.6000 1.00800
>>> 88 AH 1 HAP H1D 16 0.6000 1.00800
>>>
>>>
>>> [ bonds ]
>>> ;aqui se ponen los enlaces que se encuentran el pdb
>>> ; ai aj funct r0 kr
>>> 29 1 1 0.154E+00 6.0706E+03
>>> 29 19 1 0.154E+00 6.0706E+03
>>> 29 25 1 0.154E+00 6.0706E+03
>>> 29 27 1 0.154E+00 6.0706E+03
>>> 30 2 1 0.154E+00 6.0706E+03
>>> 30 20 1 0.154E+00 6.0706E+03
>>> 30 26 1 0.154E+00 6.0706E+03
>>> 30 28 1 0.154E+00 6.0706E+03
>>> 37 3 1 0.154E+00 6.0706E+03
>>> 37 21 1 0.154E+00 6.0706E+03
>>> 37 33 1 0.154E+00 6.0706E+03
>>> 37 35 1 0.154E+00 6.0706E+03
>>> 38 4 1 0.154E+00 6.0706E+03
>>> 38 22 1 0.154E+00 6.0706E+03
>>> 38 34 1 0.154E+00 6.0706E+03
>>> 38 36 1 0.154E+00 6.0706E+03
>>> 45 5 1 0.154E+00 6.0706E+03
>>> 45 23 1 0.154E+00 6.0706E+03
>>> 45 41 1 0.154E+00 6.0706E+03
>>> 45 43 1 0.154E+00 6.0706E+03
>>> 46 6 1 0.154E+00 6.0706E+03
>>> 46 24 1 0.154E+00 6.0706E+03
>>> 46 42 1 0.154E+00 6.0706E+03
>>> 46 44 1 0.154E+00 6.0706E+03
>>> 53 7 1 0.154E+00 6.0706E+03
>>> 53 13 1 0.154E+00 6.0706E+03
>>> 53 49 1 0.154E+00 6.0706E+03
>>> 53 51 1 0.154E+00 6.0706E+03
>>> 54 8 1 0.154E+00 6.0706E+03
>>> 54 14 1 0.154E+00 6.0706E+03
>>> 54 50 1 0.154E+00 6.0706E+03
>>> 54 52 1 0.154E+00 6.0706E+03
>>> 61 9 1 0.154E+00 6.0706E+03
>>> 61 15 1 0.154E+00 6.0706E+03
>>> 61 57 1 0.154E+00 6.0706E+03
>>> 61 59 1 0.154E+00 6.0706E+03
>>> 62 10 1 0.154E+00 6.0706E+03
>>> 62 16 1 0.154E+00 6.0706E+03
>>> 62 58 1 0.154E+00 6.0706E+03
>>> 62 60 1 0.154E+00 6.0706E+03
>>> 69 11 1 0.154E+00 6.0706E+03
>>> 69 17 1 0.154E+00 6.0706E+03
>>> 69 65 1 0.154E+00 6.0706E+03
>>> 69 67 1 0.154E+00 6.0706E+03
>>> 70 12 1 0.154E+00 6.0706E+03
>>> 70 18 1 0.154E+00 6.0706E+03
>>> 70 66 1 0.154E+00 6.0706E+03
>>> 70 68 1 0.154E+00 6.0706E+03
>>> 81 83 1 0.09600E+00 1.25317e+04
>>> 82 84 1 0.09600E+00 1.25317e+04
>>> 85 87 1 0.09600E+00 1.25317e+04
>>> 86 88 1 0.09600E+00 1.25317e+04
>>>
>>>
>>> [ pairs ]
>>> ; ai aj funct
>>>
>>> [ angles ]
>>> ;aqui se ponen los angulos posibles entre los enlaces
>>> ; ai aj ak funct 0 k0
>>> 1 29 19 1 1.911E+00 4.973342e+04
>>> 1 29 25 1 1.911E+00 4.973342e+04
>>> 1 29 27 1 1.911E+00 4.973342e+04
>>> 19 29 25 1 1.911E+00 4.973342e+04
>>> 19 29 27 1 1.911E+00 4.973342e+04
>>> 25 29 27 1 1.911E+00 4.973342e+04
>>> 2 30 20 1 1.911E+00 4.973342e+04
>>> 2 30 26 1 1.911E+00 4.973342e+04
>>> 2 30 28 1 1.911E+00 4.973342e+04
>>> 20 30 26 1 1.911E+00 4.973342e+04
>>> 20 30 28 1 1.911E+00 4.973342e+04
>>> 26 30 28 1 1.911E+00 4.973342e+04
>>> 3 37 21 1 1.911E+00 4.973342e+04
>>> 3 37 33 1 1.911E+00 4.973342e+04
>>> 3 37 35 1 1.911E+00 4.973342e+04
>>> 21 37 33 1 1.911E+00 4.973342e+04
>>> 21 37 35 1 1.911E+00 4.973342e+04
>>> 33 37 35 1 1.911E+00 4.973342e+04
>>> 4 38 22 1 1.911E+00 4.973342e+04
>>> 4 38 34 1 1.911E+00 4.973342e+04
>>> 4 38 36 1 1.911E+00 4.973342e+04
>>> 22 38 34 1 1.911E+00 4.973342e+04
>>> 22 38 36 1 1.911E+00 4.973342e+04
>>> 34 38 36 1 1.911E+00 4.973342e+04
>>> 5 45 23 1 1.911E+00 4.973342e+04
>>> 5 45 41 1 1.911E+00 4.973342e+04
>>> 5 45 43 1 1.911E+00 4.973342e+04
>>> 23 45 41 1 1.911E+00 4.973342e+04
>>> 23 45 43 1 1.911E+00 4.973342e+04
>>> 41 45 43 1 1.911E+00 4.973342e+04
>>> 6 46 24 1 1.911E+00 4.973342e+04
>>> 6 46 42 1 1.911E+00 4.973342e+04
>>> 6 46 44 1 1.911E+00 4.973342e+04
>>> 24 46 42 1 1.911E+00 4.973342e+04
>>> 24 46 44 1 1.911E+00 4.973342e+04
>>> 42 46 44 1 1.911E+00 4.973342e+04
>>> 7 53 13 1 1.911E+00 4.973342e+04
>>> 7 53 49 1 1.911E+00 4.973342e+04
>>> 7 53 51 1 1.911E+00 4.973342e+04
>>> 13 53 49 1 1.911E+00 4.973342e+04
>>> 13 53 51 1 1.911E+00 4.973342e+04
>>> 49 53 51 1 1.911E+00 4.973342e+04
>>> 8 54 14 1 1.911E+00 4.973342e+04
>>> 8 54 50 1 1.911E+00 4.973342e+04
>>> 8 54 52 1 1.911E+00 4.973342e+04
>>> 14 54 50 1 1.911E+00 4.973342e+04
>>> 14 54 52 1 1.911E+00 4.973342e+04
>>> 50 54 52 1 1.911E+00 4.973342e+04
>>> 9 61 15 1 1.911E+00 4.973342e+04
>>> 9 61 57 1 1.911E+00 4.973342e+04
>>> 9 61 59 1 1.911E+00 4.973342e+04
>>> 15 61 57 1 1.911E+00 4.973342e+04
>>> 15 61 59 1 1.911E+00 4.973342e+04
>>> 57 61 59 1 1.911E+00 4.973342e+04
>>> 10 62 16 1 1.911E+00 4.973342e+04
>>> 10 62 58 1 1.911E+00 4.973342e+04
>>> 10 62 60 1 1.911E+00 4.973342e+04
>>> 16 62 58 1 1.911E+00 4.973342e+04
>>> 16 62 60 1 1.911E+00 4.973342e+04
>>> 58 62 60 1 1.911E+00 4.973342e+04
>>> 11 69 17 1 1.911E+00 4.973342e+04
>>> 11 69 65 1 1.911E+00 4.973342e+04
>>> 11 69 67 1 1.911E+00 4.973342e+04
>>> 17 69 65 1 1.911E+00 4.973342e+04
>>> 17 69 67 1 1.911E+00 4.973342e+04
>>> 65 69 67 1 1.911E+00 4.973342e+04
>>> 12 70 18 1 1.911E+00 4.973342e+04
>>> 12 70 66 1 1.911E+00 4.973342e+04
>>> 12 70 68 1 1.911E+00 4.973342e+04
>>> 18 70 66 1 1.911E+00 4.973342e+04
>>> 18 70 68 1 1.911E+00 4.973342e+04
>>> 66 70 68 1 1.911E+00 4.973342e+04
>>>
>>> [ dihedrals ]
>>> ; ai aj ak al funct phi0 cp mult
>>>
>>> ; Include Position restraint file
>>> ;#ifdef POSRES_HAP
>>> ;#include "hap_posre.itp"
>>> ;#endif
>>>
>>>
>>> 3- hap_posre.itp
>>> ; position restraints for HAP of Generated by trjconv :
>>> Model-4-HAP-scelda2-100-10bx5c t= 0.00000
>>>
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000000 1000000 1000000
>>> 2 1 1000000 1000000 1000000
>>> 3 1 1000000 1000000 1000000
>>> 4 1 1000000 1000000 1000000
>>> 5 1 1000000 1000000 1000000
>>> 6 1 1000000 1000000 1000000
>>> 7 1 1000000 1000000 1000000
>>> 8 1 1000000 1000000 1000000
>>> 9 1 1000000 1000000 1000000
>>> 10 1 1000000 1000000 1000000
>>> 11 1 1000000 1000000 1000000
>>> 12 1 1000000 1000000 1000000
>>> 13 1 1000000 1000000 1000000
>>> 14 1 1000000 1000000 1000000
>>> 15 1 1000000 1000000 1000000
>>> 16 1 1000000 1000000 1000000
>>> 17 1 1000000 1000000 1000000
>>> 18 1 1000000 1000000 1000000
>>> 19 1 1000000 1000000 1000000
>>> 20 1 1000000 1000000 1000000
>>> 21 1 1000000 1000000 1000000
>>> 22 1 1000000 1000000 1000000
>>> 23 1 1000000 1000000 1000000
>>> 24 1 1000000 1000000 1000000
>>> 25 1 1000000 1000000 1000000
>>> 26 1 1000000 1000000 1000000
>>> 27 1 1000000 1000000 1000000
>>> 28 1 1000000 1000000 1000000
>>> 29 1 1000000 1000000 1000000
>>> 30 1 1000000 1000000 1000000
>>> 31 1 1000000 1000000 1000000
>>> 32 1 1000000 1000000 1000000
>>> 33 1 1000000 1000000 1000000
>>> 34 1 1000000 1000000 1000000
>>> 35 1 1000000 1000000 1000000
>>> 36 1 1000000 1000000 1000000
>>> 37 1 1000000 1000000 1000000
>>> 38 1 1000000 1000000 1000000
>>> 39 1 1000000 1000000 1000000
>>> 40 1 1000000 1000000 1000000
>>> 41 1 1000000 1000000 1000000
>>> 42 1 1000000 1000000 1000000
>>> 43 1 1000000 1000000 1000000
>>> 44 1 1000000 1000000 1000000
>>> 45 1 1000000 1000000 1000000
>>> 46 1 1000000 1000000 1000000
>>> 47 1 1000000 1000000 1000000
>>> 48 1 1000000 1000000 1000000
>>> 49 1 1000000 1000000 1000000
>>> 50 1 1000000 1000000 1000000
>>> 51 1 1000000 1000000 1000000
>>> 52 1 1000000 1000000 1000000
>>> 53 1 1000000 1000000 1000000
>>> 54 1 1000000 1000000 1000000
>>> 55 1 1000000 1000000 1000000
>>> 56 1 1000000 1000000 1000000
>>> 57 1 1000000 1000000 1000000
>>> 58 1 1000000 1000000 1000000
>>> 59 1 1000000 1000000 1000000
>>> 60 1 1000000 1000000 1000000
>>> 61 1 1000000 1000000 1000000
>>> 62 1 1000000 1000000 1000000
>>> 63 1 1000000 1000000 1000000
>>> 64 1 1000000 1000000 1000000
>>> 65 1 1000000 1000000 1000000
>>> 66 1 1000000 1000000 1000000
>>> 67 1 1000000 1000000 1000000
>>> 68 1 1000000 1000000 1000000
>>> 69 1 1000000 1000000 1000000
>>> 70 1 1000000 1000000 1000000
>>> 71 1 1000000 1000000 1000000
>>> 72 1 1000000 1000000 1000000
>>> 73 1 1000000 1000000 1000000
>>> 74 1 1000000 1000000 1000000
>>> 75 1 1000000 1000000 1000000
>>> 76 1 1000000 1000000 1000000
>>> 77 1 1000000 1000000 1000000
>>> 78 1 1000000 1000000 1000000
>>> 79 1 1000000 1000000 1000000
>>> 80 1 1000000 1000000 1000000
>>> 81 1 1000000 1000000 1000000
>>> 82 1 1000000 1000000 1000000
>>> 83 1 1000000 1000000 1000000
>>> 84 1 1000000 1000000 1000000
>>> 85 1 1000000 1000000 1000000
>>> 86 1 1000000 1000000 1000000
>>> 87 1 1000000 1000000 1000000
>>> 88 1 1000000 1000000 1000000
>>>
>>> 4- topol.top
>>> ; Include forcefield parameters
>>> #include "gromos_HAP.ff/forcefield.itp"
>>>
>>>
>>> ; Include HAP crystal slap topology
>>> #include "HAP-MODEL4-100.itp"
>>> #ifdef POSRES_HAP
>>> #include "hap_posre.itp"
>>> #endif
>>>
>>>
>>> ; Include water topology
>>> #include "gromos53a6_HAP.ff/spc.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000 1000 1000
>>> #endif
>>>
>>> ; Include topology for ions
>>> #include "gromos53a6_HAP.ff/ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> newbox-pep2 in water
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> HAP 1
>>>
>>> Looking forward to your comments...
>>>
>>> Cheers,
>>> Ramon
>>>
>>>
>>> On Wed, 25 Jul 2012 15:10:43 -0400, Justin Lemkul wrote
>>>> On 7/25/12 2:32 PM, Ramon Garduno wrote:
>>>>> Dear gmx friends:
>>>>>
>>>>> We are modeling a solvated hydroxyapatite(HAP)-protein complex. We have
>>>>> minimized and equilibrated this system to 300K under NVT.
>>>>>
>>>>> The odd behavior is observed when we start an NPT simulation. In the very
>>>>> first ps we observed that the oxygens bound (initially) to phosphorous in
>>>>> phosphate tetrahedon assume a geometry in which all four oxygens are grouped
>>>>> together like this P=O, however we never receive an error message.
>>>>>
>>>>> The bond lenghts have been constrained using the SHAKE algorithm.
>>>>>
>>>>> HAP is in the form of a crystal slab. The HAP parameters we have used were
>>>>> taken from Dinesh-Katti's paper [Polymer 48 (2007) 664-674], in turn, Katti
>>>>> took the HAP parameters from Hauptmann [Phys Chem Chem Phys (2003) 5,
>>> 635-639].
>>>>>
>>>>> Katti's parameters were parameterized to CVFF. We have made
> ​​the
>>>>> corresponding unit convertions to fit those requiered in GROMACS v4.5. In
>>>>> short, we have used NON_BONDED (Homonuclear and Heteronuclear van der Waals
>>>>> terms), BONDED parameters (ffnonbonded.itp and HAP.itp), and the same
> PARTIAL
>>>>> ATOMIC CHARGES as those reported by Katti's group.
>>>>>
>>>>> In order to avoid the odd behaviour observed in the tetrahedral
> phosphate, we
>>>>> have used strong position restraints but the odd behaviour is still present.
>>>>> We also used freeze groups but with this command it is not possible to
>>>>> equilibrate the system under NPT.
>>>>>
>>>>> Do you have some suggestions to solve this problem?
>>>>>
>>>>
>>>> It sounds like a topology error, but without seeing the .itp file,
>>>> it's hard to guess.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> --
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>>>
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>>> Open WebMail Project (http://openwebmail.org)
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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