HI Carlos,
Thanks for the advice, I will tread carefully!
Dr Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
SB - ISIC - LCBC
BCH 4108
CH - 1015 Lausanne
On May 10, 2007, at 3:39 PM, Carlos Simmerling wrote:
> you're right- in multisander.f there is a parameter "size" that is
> 10,000.
> it should be checked against system size but isn't, we'll have to
> change
> it to be dynamically allocated. For now you can just increase it to
> 20k and recompile.
>
> I should point out that your systems looks way bigger than anything
> we've tested,
> so you'll need to be careful. REMD on something that big is really
> a research
> problem, you are likely to still have huge sampling problems. I
> guess what
> I mean is that I hope you are really familiar with REMD and
> standard simulations
> before doing this.
> carlos
>
> On 5/10/07, Geoff Wood < geoffrey.wood.epfl.ch> wrote:
> Hi Carlos,
>
>
> Yes I have, they are different and irregular. By that I mean the
> restart files for different replicas have different numbers of
> atoms specified.
>
> I have been able to get the my hybrid calculation going by reducing
> the number of kept waters from 350 to 50 and also the total number
> of waters from approx 14,000 to approx 9000. So i was wondering if
> there was an array-size issue somewhere?
>
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On May 10, 2007, at 1:20 PM, Carlos Simmerling wrote:
>
>> have you checked the number of atoms in your strip prmtop and
>> compared to the # of atoms sander is producing in the .strip restart
>> files?
>>
>> On 5/9/07, Geoff Wood <geoffrey.wood.epfl.ch> wrote:
>> Hi Carlos,
>>
>> Thanks for clearing up that issue for me. I just wanted to return
>> to the original problem I was having. For my system, I have a
>> full periodic set of files and a set of files for the stripped non-
>> periodic system. I also have a coordinate file for the stripped
>> system, since I created the parm and the corresponding crd files
>> in leap.
>>
>> If I forget about running the hybrid calculation and run a
>> standard remd simulation on the full system then it runs without
>> problems. Alternatively, if I run a standard remd run on the
>> reduced system then it also runs without problems. This suggests
>> that there is no problems with my crd or parm files in both cases.
>>
>> However, when I attempt to run the hybrid calculation then I get
>> the error that I reported. From our correspondence would you be
>> able to shed light on why this may be happening?
>>
>> Cheers,
>>
>> Dr Geoffrey Wood
>> Ecole Polytechnique Fédérale de Lausanne
>> SB - ISIC - LCBC
>> BCH 4108
>> CH - 1015 Lausanne
>>
>>
>>
>>
>> On May 9, 2007, at 11:18 PM, Carlos Simmerling wrote:
>>
>>> exactly. you need to be careful because they may not actually
>>> have full solvent shells.
>>> also you need to make sure you keep enough water to solvate both
>>> solutes.
>>>
>>> On 5/9/07, Geoff Wood < geoffrey.wood.epfl.ch> wrote:
>>> Hi Carlos,
>>>
>>> Thankyou for your response to my questions. I am still slightly
>>> confused (its just not only sander) so I just wanted to clarify
>>> what you have said. Sander should be able to run the simulation
>>> with multiple solutes but it is unclear how meaningful the
>>> results will be?
>>>
>>> Dr Geoffrey Wood
>>> Ecole Polytechnique Fédérale de Lausanne
>>> SB - ISIC - LCBC
>>> BCH 4108
>>> CH - 1015 Lausanne
>>>
>>>
>>>
>>>
>>> On May 9, 2007, at 10:52 PM, Carlos Simmerling wrote:
>>>
>>>> Hi Geoff, yes that's true, I think that it's not so much that
>>>> sander will get confused as it might
>>>> cause problems in the centering/imaging and possible inability
>>>> to get a single set of
>>>> coordinates with a complete solvent shell around multiple
>>>> solutes. This isn't a problem in the
>>>> fully solvated system during MD due to the periodicity, but the
>>>> hybrid calculation
>>>> is done without periodicity. As far as ions go, I think one
>>>> needs to have the same
>>>> caution as with explicit counterions and any implicit solvent-
>>>> we're not sure how well
>>>> they work or what the limitations are, so treat it cautiously
>>>> and only try it after you're
>>>> sure you understand what you are doing without them.
>>>> carlos
>>>>
>>>> On 5/9/07, Geoff Wood < geoffrey.wood.epfl.ch> wrote:
>>>> Hello Asim,
>>>>
>>>> Thank you very much for your suggestions they were very
>>>> helpful. I have made sure that the topology and number of
>>>> waters correspond to what sander is expecting. That being said,
>>>> I haven't been able to make much progress. If I understand your
>>>> email correctly then any attempt to run hybrid remd with counter-
>>>> ions will cause sander to get confused as to what is solute and
>>>> solvent? If this is the case, then would the same be true if I
>>>> decided to run a hybrid remd run with more than one solute (say
>>>> a dimer of two proteins)?
>>>>
>>>> Thanks in advance,
>>>>
>>>> Dr Geoffrey Wood
>>>> Ecole Polytechnique Fédérale de Lausanne
>>>> SB - ISIC - LCBC
>>>> BCH 4108
>>>> CH - 1015 Lausanne
>>>>
>>>>
>>>>
>>>>
>>>> On May 9, 2007, at 9:07 PM, Asim Okur wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Before running Hybrid Solvent REMD you should read the manual
>>>>> and the
>>>>> article (Okur, Roe, Cui, Hornak and Simmerling, JCTC, 2007)
>>>>> especially
>>>>> the warnings in the manual (Page 168).
>>>>>
>>>>> Your hybrid topology file should have exactly the same number of
>>>>> waters as the reduced system generated by sander. Use of
>>>>> counterions
>>>>> has not been implemented/tested with hybrid remd and should not be
>>>>> used.
>>>>>
>>>>> Also, I see in your GB calculations (mdin.rep01.strip) you set
>>>>> nstlim
>>>>> = 1000. You should not do any dynamics during the GB step. Just
>>>>> single
>>>>> step energy evaluation is needed. You can see examples of input
>>>>> files
>>>>> in the remd and hybrid remd test cases in amber9.
>>>>>
>>>>> I hope this helps,
>>>>>
>>>>> Asim
>>>>>
>>>>> --
>>>>> Asim Okur, Ph.D.
>>>>> Stony Brook University
>>>>> Chemistry Department
>>>>> Stony Brook, NY 11733
>>>>> (631) 632 1560
>>>>>
>>>>>
>>>>> On 5/9/07, Geoff Wood < geoffrey.wood.epfl.ch> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Slightly from first email but essentially the same:
>>>>>>
>>>>>>
>>>>>> To whom it may concern,
>>>>>>
>>>>>> I am attempting to run hybrid remd simulations with amber 9
>>>>>> but I find that
>>>>>> I cannot get them started. I am probably making a simple
>>>>>> mistake in the
>>>>>> specification of the file names, any help would be much
>>>>>> appreciated.
>>>>>>
>>>>>> The error I am getting is the following:
>>>>>>
>>>>>> -----------------------------------------------------------------
>>>>>> ---------------
>>>>>> 3. ATOMIC COORDINATES AND VELOCITIES
>>>>>> -----------------------------------------------------------------
>>>>>> ---------------
>>>>>>
>>>>>>
>>>>>> FATAL: NATOM mismatch in coord and topology files
>>>>>>
>>>>>>
>>>>>> This error appears in the stripped output file (i.e. a file
>>>>>> called something
>>>>>> like mdout.rep01.strip)
>>>>>> In the full output file it looks as if the calculation has
>>>>>> finished (the
>>>>>> file is called mdout.rep01) i.e.
>>>>>>
>>>>>> Exiting runmd after getting initial energies for
>>>>>> REMD 0
>>>>>> wrapping first mol.: 1.009557807795775E-014 68.4142020000000
>>>>>> 96.4591000000000
>>>>>>
>>>>>> -----------------------------------------------------------------
>>>>>> ---------------
>>>>>> 5. TIMINGS
>>>>>> -----------------------------------------------------------------
>>>>>> ---------------
>>>>>>
>>>>>> |>>>>>>>>PROFILE of Average TIMES>>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> The groupfile looks like
>>>>>>
>>>>>> -O -i mdin.rep01 -o mdout.rep01 -p prm -c inpcrd.rep01 -r
>>>>>> restrt.rep01 -x
>>>>>> mdcrd.rep01 -inf mdinfo.rep01
>>>>>> .
>>>>>> .
>>>>>> .
>>>>>> .
>>>>>>
>>>>>> The input files look like:
>>>>>>
>>>>>> Full box (mdin.rep01)
>>>>>>
>>>>>> comment
>>>>>> &cntrl
>>>>>> imin = 0, irest = 1, ntx = 2,
>>>>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>>>>> taup = 2.0,
>>>>>> cut = 10, ntr = 0,
>>>>>> ntc = 2, ntf = 2,
>>>>>> tempi = 0.0, temp0 = 300.0,
>>>>>> ntt = 3, gamma_ln = 1.0,
>>>>>> repcrd=0, numexchg=40, numwatkeep=350,
>>>>>> nstlim = 1000, dt = 0.002,
>>>>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>>>>> &end
>>>>>> &ewald
>>>>>> &end
>>>>>>
>>>>>> Reduced number of waters ( mdin.rep01.strip)
>>>>>>
>>>>>> comment
>>>>>> &cntrl
>>>>>> imin = 0, irest = 1, ntx = 2,
>>>>>> ntb = 0,
>>>>>> igb=1,
>>>>>> cut = 999, ntr = 0,
>>>>>> ntc = 2, ntf = 2,
>>>>>> tempi = 0.0, temp0 = 366.0,
>>>>>> ntt = 3, gamma_ln = 1.0,
>>>>>> repcrd=0, numexchg=40, numwatkeep=350,
>>>>>> nstlim = 1000, dt = 0.002,
>>>>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>>>>> /
>>>>>>
>>>>>>
>>>>>> I have placed both the full parm file (prm) and reduced parm file
>>>>>> (prm.strip) in the same directory. For the stripped parm I
>>>>>> have tried with
>>>>>> and without the counter ions that are present in the full
>>>>>> calculation. I
>>>>>> think it is preferable to omit them in a GB energy
>>>>>> evaluation. The stripped
>>>>>> parm was made using leap and a pdb that ptraj generated from
>>>>>> a short md run
>>>>>> involving the full system.
>>>>>>
>>>>>> The input coordinates are for the full system ( from a short
>>>>>> md run for
>>>>>> equilibration) and are placed in the same directory as
>>>>>> inpcrd.rep01 etc.
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>>
>>>>>> Dr Geoffrey Wood
>>>>>> Ecole Polytechnique Fédérale de Lausanne
>>>>>> SB - ISIC - LCBC
>>>>>> BCH 4108
>>>>>> CH - 1015 Lausanne
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> ------------------------------------------------------------------
>>>>> -----
>>>>> The AMBER Mail Reflector
>>>>> To post, send mail to amber.scripps.edu
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>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail:
> carlos.simmerling.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
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Received on Sun May 13 2007 - 06:07:29 PDT
