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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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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