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
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 13 2007 - 06:07:14 PDT
