[gmx-users] Force Calculation - SBLOCKS
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jun 22 03:15:37 CEST 2007
Justin M. Shorb wrote:
> Greetings!
>
> I have been running gromacs to simulate a chromophore (NMAd) in water. I
> have verified that the coulombic force is calculated correctly by doing
> a rerun of the simulation trajectory and extracting the forces from a
> forcefield of vanishing force constants (thus removing all vdW and
> bonded terms). This works, although it is fairly brute-force.
>
> Now, I am trying to scale up and look at a single peptide Amide-I band
> in a transmembrane protein. Unfortunately, if I use the same mdp file, I
> get different results than if I use the mdp file with which the
> production run was generated.
I don't understand your meaning here.
> By gmxdump-ing the tpr files, I can figure
> out the differences between the run files. I verified that varying PME
> parameters cause a negligible effect, and most of the basic I/O
> parameters of course shouldn't matter.
>
> The biggest difference between the two files is that one reports zero
> for the multinr and uses nr=0 and nra=0, whereas the other tpr file
> reports 123 for the multinr, nr=123, nra=6326, and then specifies
> blocks[SBLOCKS][...]
Um, no there are huge differences here. One uses temperature and
pressure coupling and the other doesn't. One has cut-offs at 1.4nm, the
other 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 single
> chromophore 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_1
> VAL44_1 ISO45_1 LEU46_1 LEU49_1 LEU31_2 LEU34_2 ISO38_2 LEU39_2 ISO41_2
> GLY43_2 VAL44_2 ISO45_2 LEU46_2 LEU49_2 LEU31_3 LEU34_3 ISO38_3 LEU39_3
> ISO41_3 GLY43_3 VAL44_3 ISO45_3 LEU46_3 LEU49_3 LEU31_4 LEU34_4 ISO38_4
> LEU39_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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 4
> 4 4 4 4 4 4 4 4 4 4 4
> 4 4 4 4 4 4 4 4 4 4
> 4 4 4 4 4 4 4 4 4 4
> 4 4 17123 (total 17283 atoms)
> 151205c150472
> < VCM : 852 10957 5474 (total 17283 atoms)
> ---
> > VCM : 17283 (total 17283 atoms)
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