Okay. Regarding your future work, the group specification stuff should
allow you to select specific atoms, specific residues, or search/find based
on specific characteristics including atom type (I know atom name is
different). I have not done this sort of stuff extensively myself, but the
old group specification stuff in pmemd should work as well as it did in
sander. I thought the description of this stuff had been dropped in amber
10, but it is actually now described in the manual in a separate section
entitled "GROUP Specification". Earlier releases (9, 8, etc.) have
basically the same info in the appendices. Anyway, I would be surprised if
you can't find some way to restrain the lipid (not to say that I have not
been surprised before...)
- Bob
----- Original Message -----
From: "Francesco Pietra" <chiendarret.gmail.com>
To: <amber.scripps.edu>
Sent: Tuesday, November 25, 2008 3:59 PM
Subject: Re: AMBER: RE: About restart amber
> Thanks for this very instructive piece. However, I decided to abandon
> GB for this large system. As Bud Dobson warned on a parallel thread,
> it was already well known that GB - at its present implementation -
> becomes much slower than explicit solvent MD. Add the deformations
> introduced by GB, which would require membrane surrogates, should it
> work.... I can not blame than myself for having assumed GB faster
> without checking the archives.
>
> MD in an explicit membrane is running fast with pmemd for the pore
> region of this protein. Once ready, I'll try the whole system with the
> pore region in a membrane and the rest in water. If too slow for my
> means, I'll leave the input for better equipped people. Probably I'll
> face too high obstacles at the equilibration stage (which is quite
> long because of the membrane) as I can't use pmemd to restrain the
> lipid. Only restraintmask - as far as I know - can deal with atom
> names (perhaps a hint for a future version of pmemd).
>
> francesco
>
>
>
> On Tue, Nov 25, 2008 at 3:27 PM, Robert Duke <rduke.email.unc.edu> wrote:
>> 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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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
>>> AALS -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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>>>>> to majordomo.scripps.edu
>>>>>
>>>>
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Received on Fri Dec 05 2008 - 16:45:47 PST
