Well, it blows up after a recentering operation triggered at step 1000 by
the default nscm value... The reason it blows up is that shake can't find a
reasonable solution for all bondlengths because some atom or atoms has moved
too much relative to other atoms. I have no idea what is specifically
happening here but I would get a high resolution trajectory (ntwx = 50 or
100) and look at it in vmd. It could be that partial restraints and
repositioning don't work well together, putting really unnatural forces on
things. I would try setting nscm to a larger number (>nstlim), just to see
what is going on, and look at the trajectories (and perhaps also something
smaller, like 100). When I use restraints, I am always restraining whole
molecules, so I don't have direct experience with what you are doing.
Another point: if your restraints are on a structure that was not centered
to start, I would think some really nasty things could happen in the first
recentering. Under ewald, repositioning is purely translational (nscm
option), and it used to fix an energy equipartition problem (Tom Cheatham's
lab has a paper on the "ewald flying ice cube"; J Comput Chem 19, pp
726-740). I am not sure about the generalized Born equivalent here, but I
would guess that turning off repositioning in a restrained run for a few
thousand steps would not be the end of the world. I would still very much
want to look at the trajectories though...
Regards - Bob
----- Original Message -----
From: "Francesco Pietra" <chiendarret.gmail.com>
To: <amber.scripps.edu>
Sent: Tuesday, November 25, 2008 3:00 AM
Subject: Re: AMBER: RE: About restart amber
> 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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>>>
>>
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Received on Fri Dec 05 2008 - 16:43:15 PST
