Answering to myself, setting additional restraints (for the pore
region, in the distorted conformation for one of the chains as it was
left from previous run), was met by vlimit exceeded. I suspect that
the procedure I followed is basically wrong. I started by assuming
that the the extracellular part was treated adequately by GB, while I
was not interested here in the pore region, which was distorted as to
one of the chains.
I am unable to detect any major deviation in EELEC WDW etc, so that I
am here for help. General settings for the MD simulation are in
previous mail on this thread, while the output, comprising the new
restraints (for pmemd), are here:
Keep pore initial chain A restrained
GROUP 4 HAS HARMONIC CONSTRAINTS 32.00000
GRP 4 RES 1 TO 41
Number of atoms in this group = 686
----- READING GROUP 5; TITLE:
Keep pore final chain A restrained
GROUP 5 HAS HARMONIC CONSTRAINTS 32.00000
GRP 5 RES 381 TO 426
Number of atoms in this group = 725
----- READING GROUP 6; TITLE:
Keep pore initial chain B restrained
etc for all other chain stretches in the pore.
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 118.000 ps
Number of triangulated 3-point waters found: 0
| Dynamic Memory, Types Used:
| Reals 771184
| Integers 1594255
| Running AMBER/MPI version on 8 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 118.200 TEMP(K) = 293.29 PRESS = 0.0
Etot = -14862.0902 EKtot = 15182.4903 EPtot = -30044.5805
BOND = 4208.2193 ANGLE = 10364.8917 DIHED = 13636.2332
1-4 NB = 4615.5997 1-4 EEL = 58027.8454 VDWAALS = -9952.6334
EELEC = -84702.6203 EGB = -27632.9571 RESTRAINT = 1390.8410
EAMBER (non-restraint) = -31435.4215
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 118.400 TEMP(K) = 292.26 PRESS = 0.0
Etot = -14549.8615 EKtot = 15128.9530 EPtot = -29678.8145
BOND = 4249.1002 ANGLE = 10497.9349 DIHED = 13714.8644
1-4 NB = 4622.1647 1-4 EEL = 57924.9207 VDWAALS = -9907.1452
EELEC = -84454.0644 EGB = -27791.1146 RESTRAINT = 1464.5248
EAMBER (non-restraint) = -31143.3393
------------------------------------------------------------------------------
NSTEP = 300 TIME(PS) = 118.600 TEMP(K) = 296.53 PRESS = 0.0
Etot = -14495.6067 EKtot = 15350.1320 EPtot = -29845.7387
BOND = 4191.7755 ANGLE = 10416.8064 DIHED = 13702.0116
1-4 NB = 4605.7994 1-4 EEL = 57951.4365 VDWAALS = -9853.8882
EELEC = -84508.8249 EGB = -27853.5374 RESTRAINT = 1502.6823
EAMBER (non-restraint) = -31348.4210
------------------------------------------------------------------------------
NSTEP = 400 TIME(PS) = 118.800 TEMP(K) = 298.18 PRESS = 0.0
Etot = -14369.6628 EKtot = 15435.1364 EPtot = -29804.7992
BOND = 4144.3264 ANGLE = 10392.7962 DIHED = 13603.8654
1-4 NB = 4617.9524 1-4 EEL = 58109.1303 VDWAALS = -9882.6587
EELEC = -84558.4946 EGB = -27780.5494 RESTRAINT = 1548.8329
EAMBER (non-restraint) = -31353.6320
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 119.000 TEMP(K) = 297.56 PRESS = 0.0
Etot = -14401.4198 EKtot = 15403.3889 EPtot = -29804.8086
BOND = 4170.8469 ANGLE = 10424.8530 DIHED = 13619.7513
1-4 NB = 4575.5432 1-4 EEL = 57982.6068 VDWAALS = -9920.2602
EELEC = -84607.0488 EGB = -27662.7872 RESTRAINT = 1611.6864
EAMBER (non-restraint) = -31416.4950
------------------------------------------------------------------------------
NSTEP = 600 TIME(PS) = 119.200 TEMP(K) = 297.37 PRESS = 0.0
Etot = -14324.9156 EKtot = 15393.5581 EPtot = -29718.4737
BOND = 4068.7054 ANGLE = 10487.9072 DIHED = 13705.9594
1-4 NB = 4664.9561 1-4 EEL = 57972.6307 VDWAALS = -9837.0587
EELEC = -84701.0042 EGB = -27673.2914 RESTRAINT = 1592.7218
EAMBER (non-restraint) = -31311.1955
------------------------------------------------------------------------------
NSTEP = 700 TIME(PS) = 119.400 TEMP(K) = 298.96 PRESS = 0.0
Etot = -14226.3546 EKtot = 15475.6550 EPtot = -29702.0096
BOND = 4114.8803 ANGLE = 10518.2858 DIHED = 13716.4825
1-4 NB = 4642.9989 1-4 EEL = 57873.1198 VDWAALS = -9909.4567
EELEC = -84559.0840 EGB = -27685.0454 RESTRAINT = 1585.8092
EAMBER (non-restraint) = -31287.8188
------------------------------------------------------------------------------
NSTEP = 800 TIME(PS) = 119.600 TEMP(K) = 297.23 PRESS = 0.0
Etot = -14338.7373 EKtot = 15386.1646 EPtot = -29724.9020
BOND = 4204.7480 ANGLE = 10420.4349 DIHED = 13658.4428
1-4 NB = 4633.6685 1-4 EEL = 57948.2947 VDWAALS = -9867.9684
EELEC = -84626.2242 EGB = -27715.7199 RESTRAINT = 1619.4217
EAMBER (non-restraint) = -31344.3237
------------------------------------------------------------------------------
NSTEP = 900 TIME(PS) = 119.800 TEMP(K) = 299.42 PRESS = 0.0
Etot = -14227.7282 EKtot = 15499.4711 EPtot = -29727.1993
BOND = 4169.8501 ANGLE = 10520.4113 DIHED = 13684.0647
1-4 NB = 4610.5941 1-4 EEL = 57995.3457 VDWAALS = -9865.9772
EELEC = -84707.6272 EGB = -27695.0750 RESTRAINT = 1561.2141
EAMBER (non-restraint) = -31288.4135
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.499075 0.005780 1.333641
NSTEP = 1000 TIME(PS) = 120.000 TEMP(K) = 299.15 PRESS = 0.0
Etot = -14292.8263 EKtot = 15485.3583 EPtot = -29778.1846
BOND = 4142.2201 ANGLE = 10420.1202 DIHED = 13702.3912
1-4 NB = 4625.8817 1-4 EEL = 58004.4484 VDWAALS = -9979.7547
EELEC = -84469.6363 EGB = -27779.4524 RESTRAINT = 1555.5971
EAMBER (non-restraint) = -31333.7817
------------------------------------------------------------------------------
vlimit exceeded for step 1025; vmax = 29.6260
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 4 984 578 576
Thanks for any advice
francesco
On Mon, Nov 24, 2008 at 10:22 PM, Francesco Pietra
<chiendarret.gmail.com> wrote:
> Hi Ross:
> As the pore region of the transmembrane protein I am dealing with gets
> deformed on long MD simulation under GB conditions (while the
> extracellular portion behaves normally), I would like to continue with
> GB by restraining the pore region (which was not comprised on last
> run). In fact, I am not interested in the pore region in these
> simulations. Is it correct to use as reference (-ref ...rst) the
> restart file of previous run while adding now the new restraints?
>
> From a trial with nstlim=1 all restraints (given as GROUP for pmemd)
> are read, as from the out file. Is anything subtly wrong that can't be
> detected this way?
>
> Thanks
> francesco
>
> On Sat, Nov 22, 2008 at 6:18 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>> Hi Francesco,
>>
>>> When restraints are imposed, which reference file should be used in
>>> running sander or pmemd again? I guess the "-ref ...rst" pertaining to
>>> the crashed job. Correct? Does that involve any further complication?
>>
>> If you want an actual restart then you should restrain to the same restart file as the original run. Note, however, that when running NPT I think this leads to instabilities since there is some kind of adjustment of the box coordinates done that then means the restraints are too large. I have never actually nailed this problem down but essentially it means for constant pressure that you can only ever restrain to the same restart file as you are using for the input coordinates (-i). I think the problem originates in the fact that when you restart the box coordinates in your inpcrd file do not match the box coordinates in your -ref file.
>>
>> At least this problem existed back in Amber 7 - maybe it got fixed, I haven't tried it in a while. I avoid running constant pressure runs with restraints anyway because I figure the restraints are effectively giving you artificial behavior anyway. E.g. suppose something wants to elongate but the restraints stop it - really the box should change size to accommodate this elongation.
>>
>> That is probably complicating things though. For NVE and NVT you should just be able to use the same -ref as you did for the previous run.
>>
>>> In view of non minor work in restarting from a crashed job while
>>> taking everything into account (not to mention the unluky situation
>>> that the machine was just writing the rst file), is any major drawback
>>> in making the various steps of MD short? If problems exist, how to
>>> determine how much short?
>>
>> You should probably read the following 'very interesting' paper:
>>
>> http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2008/4/i10/abs/ct8002173.html
>>
>> This looks at problems with repeating random number sequences and Langevin / Andersen dynamics, the equivalent behavior that occurs when you continually restart a simulation so effectively running very short MD runs. The key problem, with continuous short restarts, is that AMBER (and CHARMM and most other codes I think) do not strictly do proper restarts. That is they do not preserve the state of the random number stream. Hence if you just keep blindly restarting you use the exact same set of random numbers each time. For NVE this is not a problem but for Langevin dynamics it can become acute because you introduce correlation (in the reuse of the random number stream) in the 'random' forces applied and this can lead to all kinds of weird behavior. For reasonably long runs between restarts the correlation is 'weak' enough that it does not adversely affect the dynamics but for short gaps between restarts you can get strange behavior.
>>
>> The main point to take home here is that you should probably 'ALWAYS' be changing the random number seed (ig=) whenever you restart a simulation - in fact you should probably never run any two MD runs with the same seed (except for testing / debugging). A simple solution to this (in AMBER 10) is to set ig=-1 and then it will use the wallclock time in microseconds to seed the random number generator.
>>
>> We should probably be more explicit about this in the manual / tutorials etc but the reality is that we are only now beginning to realize that such effects exist.
>>
>> Good luck,
>> Ross
>>
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
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Received on Fri Dec 05 2008 - 16:40:43 PST
