[gmx-users] Lincs again
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Thu May 12 16:20:29 CEST 2005
Sorry for that this simulation is 50ns i don't update it in my mdp file
... anyway all after ";"
is a comment ;-)
Kai Zhuang wrote:
>hi,
>i' new to Gromacs and MD (only been looking at it for a week)
>i have a question about ur mdp script...
>
>
>>dt = 0.002 ; ps !
>>nsteps = 25000000 ; total 100 ps.
>>
>>
>how is 25000000 * 0.002 = 100? the unit is ps right?
>thx
>Kai
>
>On 5/12/05, Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu> wrote:
>
>
>>I understand that but the initial structure i got from a previous
>>simulation (30ns) that crash because
>>lot of LINCS warnings then i got the final structure do a minimization
>>and then crash again after 2ns
>>my question is Why happens after 30ns its a big time?
>>i will try your suggestion?
>>
>>Thanks
>>
>>Osmany
>>
>>
>>Haberl Florian wrote:
>>
>>
>>
>>>Hi
>>>
>>>search gromacs mail archive, if your protein is not enough "relaxed" than
>>>this will always appear, so do further energy minimisation and/ or
>>>simulation with position restraining.
>>>
>>>
>>>
>>>
>>>
>>>>hi again
>>>>similiar to the previous mail i am doing other simulation of other
>>>>protein and again got tha same error
>>>>with LINCS
>>>>
>>>>Constraint error in algorithm Lincs at step 973112
>>>>
>>>>Step 973113, time 1946.23 (ps) LINCS WARNING
>>>>relative constraint deviation after LINCS:
>>>>max 20.680283 (between atoms 1449 and 1451) rms 0.741946
>>>>bonds that rotated more than 30 degrees:
>>>>atom 1 atom 2 angle previous, current, constraint length
>>>> 1429 1438 32.0 0.1571 0.1867 0.1530
>>>> 1438 1439 37.8 0.1263 0.1525 0.1230
>>>> 1438 1440 30.9 0.1318 0.1991 0.1330
>>>> 1440 1441 100.1 0.0564 0.2241 0.1000
>>>> 1440 1442 137.7 0.3441 0.7378 0.1470
>>>> 1442 1443 152.1 0.4083 1.0938 0.1530
>>>> 1442 1449 175.9 0.6039 1.8333 0.1530
>>>> 1443 1444 95.7 0.5500 0.9234 0.1530
>>>> 1444 1445 83.9 0.9134 0.6641 0.1230
>>>> 1444 1446 86.0 0.1825 0.7594 0.1330
>>>> 1446 1447 95.4 0.2018 0.1982 0.1000
>>>> 1446 1448 96.6 0.3461 0.1610 0.1000
>>>> 1449 1450 147.5 0.4649 1.9323 0.1230
>>>> 1449 1451 153.6 0.4008 2.8835 0.1330
>>>> 1451 1452 164.0 0.1313 1.9797 0.1470
>>>> 1451 1455 164.5 0.2039 1.7734 0.1470
>>>> 1452 1456 82.4 0.1670 0.6218 0.1530
>>>> 1453 1454 59.0 0.1566 0.2983 0.1530
>>>> 1454 1455 41.8 0.1490 0.5385 0.1530
>>>> 1458 1459 88.5 0.1168 0.1112 0.1000
>>>>Constraint error in algorithm Lincs at step 973113
>>>>
>>>>Step 973114, time 1946.23 (ps) LINCS WARNING
>>>>relative constraint deviation after LINCS:
>>>>max 5468.159180 (between atoms 1442 and 1449) rms 243.802231
>>>>bonds that rotated more than 30 degrees:
>>>>atom 1 atom 2 angle previous, current, constraint length
>>>> 1422 1424 44.1 0.1473 0.2103 0.1470
>>>> 1424 1425 79.9 0.1544 2.8279 0.1530
>>>> 1425 1426 60.6 0.1215 2.8025 0.1230
>>>> 1425 1427 92.2 0.1415 3.8149 0.1330
>>>> 1427 1428 84.9 0.0994 4.5696 0.1000
>>>> 1429 1430 73.3 0.1364 18.4517 0.1530
>>>> 1429 1438 86.6 0.1870 74.3095 0.1530
>>>> 1430 1431 151.4 0.1659 1.2032 0.1530
>>>> 1432 1433 43.5
>>>>
>>>>
>>>>
>>>>etc etc
>>>>
>>>>What i am doing wrong
>>>>
>>>>this is may mdp file
>>>>
>>>>cpp = /lib/cpp
>>>>constraints = all-bonds
>>>>integrator = md
>>>>dt = 0.002 ; ps !
>>>>nsteps = 25000000 ; total 100 ps.
>>>>nstcomm = 1
>>>>nstxout = 6000
>>>>nstvout = 6000
>>>>;nstfout = 0
>>>>
>>>>nstxtcout = 1000
>>>>xtc_precision = 1000
>>>>xtc_grps = protein
>>>>
>>>>nstlist = 5
>>>>
>>>>;Energy Groups
>>>>;energygrps = protein ligand sol
>>>>energygrps = protein sol
>>>>
>>>>ns_type = grid
>>>>coulombtype = cut-off
>>>>rlist = 0.9
>>>>rvdw = 1.4
>>>>rcoulomb = 1.4
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>; Berendsen temperature coupling is on in three groups
>>>>Tcoupl = berendsen
>>>>tau_t = 0.1 0.1 0.1
>>>>tc_grps = protein sol NA+
>>>>ref_t = 300 300 300
>>>>
>>>>; Pressure coupling is on
>>>>Pcoupl = berendsen
>>>>pcoupltype = isotropic
>>>>tau_p = 0.5
>>>>compressibility = 4.5e-5
>>>>ref_p = 1.0
>>>>
>>>>; Generate velocites is on at 300 K.
>>>>gen_vel = no
>>>>gen_temp = 300.0
>>>>gen_seed = 173529
>>>>
>>>>
>>>>_______________________________________________
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>>>>
>>>>
>>>------------------------------------------------------------------------
>>>Florian Haberl Universitaet Erlangen/Nuernberg
>>>Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen
>>>
>>>Mailto: florian.haberl AT chemie.uni-erlangen.de
>>>
>>>------------------------------------------------------------------------
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