Re: [gmx-users] Force Calculation - SBLOCKS

Mark Abraham Thu, 21 Jun 2007 18:16:16 -0700

Justin M. Shorb wrote:

Greetings!
I have been running gromacs to simulate a chromophore (NMAd) in water. Ihave verified that the coulombic force is calculated correctly by doinga rerun of the simulation trajectory and extracting the forces from aforcefield of vanishing force constants (thus removing all vdW andbonded terms). This works, although it is fairly brute-force.
Now, I am trying to scale up and look at a single peptide Amide-I bandin a transmembrane protein. Unfortunately, if I use the same mdp file, Iget different results than if I use the mdp file with which theproduction run was generated.


I don't understand your meaning here.

By gmxdump-ing the tpr files, I can figureout the differences between the run files. I verified that varying PMEparameters cause a negligible effect, and most of the basic I/Oparameters of course shouldn't matter.
The biggest difference between the two files is that one reports zerofor the multinr and uses nr=0 and nra=0, whereas the other tpr filereports 123 for the multinr, nr=123, nra=6326, and then specifiesblocks[SBLOCKS][...]

Um, no there are huge differences here. One uses temperature andpressure coupling and the other doesn't. One has cut-offs at 1.4nm, theother 1nm. There's many more as well....


Mark

====
1c1
< PM/memb.tpr: Run with the T-coupling groups, etc.
---
> cd3z_mdr2.tpr: Run with nothing fancy, mdr file from the singlechromophore in water
15c15
<       nsteps               = 20000
---
 >       nsteps               = 0
18c18
<       nstlist              = 10
---
 >       nstlist              = 1
22c22
<       nstcomm              = 10
---
 >       nstcomm              = 1
24,30c24,30
<       nstcheckpoint        = 10
<       nstlog               = 10
<       nstxout              = 10
<       nstvout              = 10
<       nstfout              = 10
<       nstenergy            = 10
<       nstxtcout            = 10
---
 >       nstcheckpoint        = 1000
 >       nstlog               = 10000
 >       nstxout              = 0
 >       nstvout              = 0
 >       nstfout              = 0
 >       nstenergy            = 10000
 >       nstxtcout            = 50000
32,38c32,38
<       delta_t              = 0.0005
<       xtcprec              = 10
<       nkx                  = 54
<       nky                  = 54
<       nkz                  = 54
<       pme_order            = 4
<       ewald_rtol           = 1e-05
---
 >       delta_t              = 0.002
 >       xtcprec              = 1000
 >       nkx                  = 32
 >       nky                  = 32
 >       nkz                  = 32
 >       pme_order            = 6
 >       ewald_rtol           = 1e-06
41c41
<       optimize_fft         = TRUE
---
 >       optimize_fft         = FALSE
45,48c45,48
<       etc                  = Nose-Hoover
<       epc                  = Parrinello-Rahman
<       epctype              = Anisotropic
<       tau_p                = 3
---
 >       etc                  = No
 >       epc                  = No
 >       epctype              = Isotropic
 >       tau_p                = 1
50,52c50,52
<          ref_p[    0]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
<          ref_p[    1]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
<          ref_p[    2]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
---
 >          ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
 >          ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
 >          ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
54,56c54,56
<          compress[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
<          compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
<          compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
---
 >          compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
 >          compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
 >          compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
58c58
<       rlist                = 1
---
 >       rlist                = 1.4
61c61
<       rcoulomb             = 1
---
 >       rcoulomb             = 1.4
64c64
<       rvdw                 = 1
---
 >       rvdw                 = 1.4
110,112c110,112
<       userint1             = 0
<       userint2             = 0
<       userint3             = 0
---
 >       userint1             = 1
 >       userint2             = 4
 >       userint3             = 40
119,123c119,123
<       nrdf:            1689       21915       11064
<       ref_t:             310         310         310
<       tau_t:             0.3         0.3         0.3
< anneal:                  No          No          No
< ann_npoints:               0           0           0
---
 >       nrdf:           40893
 >       ref_t:               0
 >       tau_t:               0
 > anneal:                  No
 > ann_npoints:               0
126,128c126
<       energygrp_flags[  0]: 0 0 0
<       energygrp_flags[  1]: 0 0 0
<       energygrp_flags[  2]: 0 0 0
---
 >       energygrp_flags[  0]: 0
159c157
<    nosehoover_xi:               0           0           0
---
 >    nosehoover_xi:               0
17445,34727c17443,34725
---
34733,34742c34731,34740
---
34747,52017c34745,52015
< grp[0] nr=3, name=[ Protein Solvent DMPC]
< grp[1] nr=3, name=[ Protein Solvent DMPC]
---
 > grp[0] nr=1, name=[ rest]
 > grp[1] nr=1, name=[ rest]
52020c52018
< grp[4] nr=1, name=[ rest]
---
> grp[4] nr=41, name=[ LEU31_1 LEU34_1 ISO38_1 LEU39_1 ISO41_1 GLY43_1VAL44_1 ISO45_1 LEU46_1 LEU49_1 LEU31_2 LEU34_2 ISO38_2 LEU39_2 ISO41_2GLY43_2 VAL44_2 ISO45_2 LEU46_2 LEU49_2 LEU31_3 LEU34_3 ISO38_3 LEU39_3ISO41_3 GLY43_3 VAL44_3 ISO45_3 LEU46_3 LEU49_3 LEU31_4 LEU34_4 ISO38_4LEU39_4 ISO41_4 GLY43_4 VAL44_4 ISO45_4 LEU46_4 LEU49_4 rest]
52022c52020
< grp[6] nr=3, name=[ Protein Solvent DMPC]
---
 > grp[6] nr=1, name=[ rest]
90461c90459
<          grpname (24):
---
 >          grpname (64):
90485c90483,90523
<             grpname[23]={name="rest"}
---
 >             grpname[23]={name="LEU31_1"}
...
 >             grpname[62]={name="LEU49_4"}
 >             grpname[63]={name="rest"}
124641,125427c124679,124681
< multinr[division over processors]: 123 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
<             nr=123
<             nra=6326
<             blocks[SBLOCKS][0][0..212]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
<                11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
<                25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
<                39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
<                53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,
<                67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
<                81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
< 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,107,< 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119,< 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,131,< 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,143,< 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,155,< 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166,167,< 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178,179,< 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190,191,< 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,203,
<                204, 205, 206, 207, 208, 209, 210, 211, 212}
...
<             blocks[SBLOCKS][4][852..897]={852, 853, 854, 855, 856, 857,
< 858, 859, 860, 861, 862, 863, 864, 865, 866, 867, 868,869,< 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880,881,< 882, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892,893,
<                894, 895, 896, 897}
<                6325}
...
---
> multinr[division over processors]: 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 >             nr=0
 >             nra=0
125431c124685
<          ntypes=9
---
 >          ntypes=22
125433,125440c124687,124707
< functype[1]=ANGLES, thA= 0.00000e+00, ctA= 0.00000e+00,thB= 0.00000e+00, ctB= 0.00000e+00< functype[2]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=2< functype[3]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=6< functype[4]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=3< functype[5]=IDIHS, xiA= 0.00000e+00, cxA= 0.00000e+00,xiB= 0.00000e+00, cxB= 0.00000e+00< functype[6]=LJ14, c6A= 0.00000000e+00, c12A=0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
<             functype[7]=CONSTR, dA= 0.00000000e+00, dB= 0.00000000e+00
<             functype[8]=SETTLE, doh= 1.00000001e-01, dhh= 1.63299993e-01
---
> functype[1]=BONDS, b0A= 0.00000e+00, cbA= 0.00000e+00,b0B= 0.00000e+00, cbB= 0.00000e+00> functype[2]=ANGLES, thA= 1.21000e+02, ctA= 0.00000e+00,thB= 1.21000e+02, ctB= 0.00000e+00> functype[3]=ANGLES, thA= 1.15000e+02, ctA= 0.00000e+00,thB= 1.15000e+02, ctB= 0.00000e+00> functype[4]=ANGLES, thA= 1.24000e+02, ctA= 0.00000e+00,thB= 1.24000e+02, ctB= 0.00000e+00> functype[5]=ANGLES, thA= 1.23000e+02, ctA= 0.00000e+00,thB= 1.23000e+02, ctB= 0.00000e+00> functype[6]=ANGLES, thA= 1.22000e+02, ctA= 0.00000e+00,thB= 1.22000e+02, ctB= 0.00000e+00> functype[7]=ANGLES, thA= 1.09500e+02, ctA= 0.00000e+00,thB= 1.09500e+02, ctB= 0.00000e+00> functype[8]=ANGLES, thA= 1.11000e+02, ctA= 0.00000e+00,thB= 1.11000e+02, ctB= 0.00000e+00> functype[9]=ANGLES, thA= 1.20000e+02, ctA= 0.00000e+00,thB= 1.20000e+02, ctB= 0.00000e+00> functype[10]=ANGLES, thA= 1.17000e+02, ctA= 0.00000e+00,thB= 1.17000e+02, ctB= 0.00000e+00> functype[11]=ANGLES, thA= 1.26000e+02, ctA= 0.00000e+00,thB= 1.26000e+02, ctB= 0.00000e+00> functype[12]=ANGLES, thA= 0.00000e+00, ctA= 0.00000e+00,thB= 0.00000e+00, ctB= 0.00000e+00> functype[13]=PDIHS, phiA= 1.80000000e+02, cpA=0.00000000e+00, phiB= 1.80000000e+02, cpB= 0.00000000e+00, mult=2> functype[14]=PDIHS, phiA= 1.80000000e+02, cpA=0.00000000e+00, phiB= 1.80000000e+02, cpB= 0.00000000e+00, mult=6> functype[15]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=3> functype[16]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=6> functype[17]=PDIHS, phiA= 0.00000000e+00, cpA=0.00000000e+00, phiB= 0.00000000e+00, cpB= 0.00000000e+00, mult=2> functype[18]=IDIHS, xiA= 0.00000e+00, cxA= 0.00000e+00,xiB= 0.00000e+00, cxB= 0.00000e+00> functype[19]=IDIHS, xiA= 3.52640e+01, cxA= 0.00000e+00,xiB= 3.52640e+01, cxB= 0.00000e+00> functype[20]=LJ14, c6A= 0.00000000e+00, c12A=0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00> functype[21]=SETTLE, doh= 1.00000001e-01, dhh=1.63299993e-01
125442c124709,130930
<             nr: 0
---
 >             nr: 18657
 >             multinr[division over processors]: 18657
 >             iatoms:
125459,133037c130947,138525
---
133052,135351c138540,140839
---
135360,136204c140848,141692
---
136211,141245c141699,146733
---
141291,147512c146779
<             nr: 18657
<             multinr[division over processors]: 18657
<             iatoms:
---
 >             nr: 0
147519,151169c146786,150436
---
151199,151200c150466,150467
< T-Coupling  :     852  10957   5474  (total 17283 atoms)
< Energy Mon. :     852  10957   5474  (total 17283 atoms)
---
 > T-Coupling  :   17283  (total 17283 atoms)
 > Energy Mon. :   17283  (total 17283 atoms)
151203c150470
< User1       :   17283  (total 17283 atoms)
---
> User1 : 4 4 4 4 4 4 44 4 4 4 4 4 4 4 4 4 44 4 4 4 4 4 4 4 4 44 4 4 4 4 4 4 4 4 44 4 17123 (total 17283 atoms)
151205c150472
< VCM         :     852  10957   5474  (total 17283 atoms)
---
 > VCM         :   17283  (total 17283 atoms)

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Re: [gmx-users] Force Calculation - SBLOCKS

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