Dear Dr. Simmerling
thanks for your reply.
I have already tested the MD without the tgtmd for both protein
conformations and it works fine.
I have also tried with just one CPU with smaller nstlim and ntpr=1 but i
have the same frozen state with the following output:
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 454224.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 454218. NUM_NOSHAKE = 0 CORRECTED RNDFP = 454218.
| TOTAL # of degrees of freedom (RNDF) = 454218.
NSTEP = 0 TIME(PS) = 120.000 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 4013136.4603 EKtot = 0.0000 EPtot =
4013136.4603
BOND = 2060.5152 ANGLE = 5811.0946 DIHED = 7670.1463
1-4 NB = 2481.8886 1-4 EEL = 22414.5833 VDWAALS = 40379.6693
EELEC = -417775.1195 EGB = -131754.0231 RESTRAINT =
4481847.7057
EAMBER (non-restraint) = -468711.2454
Current RMSD from reference: 18.248
Current target RMSD: 0.000
My concern are about the Current RMSD from reference value it should be 2.
thank you very much
Antonio
On 12/22/2014 02:42 PM, Carlos Simmerling wrote:
> if you haven't already done this, I suggest (1) making sure MD without the
> tgtmd works fine using the same input coordinates and (2) try the tgtmd
> using sander with a single CPU and shorter nstlim, with ntpr=1 so you can
> get a better idea of whether something is wrong with the energies. also,
> what is your reference coordinate set?
>
> On Mon, Dec 22, 2014 at 8:31 AM, antonio.coluccia.uniroma1.it <
> antonio.coluccia.uniroma1.it> wrote:
>> Dear All,
>> I would like to carry out a target dynamics.
>> Following suggestion fro the mailing list
>> i have computed parameters for starting and reference conformations of
>> studied protein with leap,
>> checked the number of atoms and computed the minimization for both
>> conformations.
>> When i use sander to carry out target dynamics calculation the system
>> was frozen at the step 0 with the RMSD higher that the real one and with
>> CPU working at 100%.
>> I suppose that the problem could be the size of the water boxes for the
>> two protein conformations
>> but i do not know how to solve the problem
>> Do you have any suggestions?
>>
>> My input file is:
>> &cntrl
>> nstlim= 10000000, dt=0.002, temp0=300.0, ntt=1,
>> ntpr=500, ntwr=5000, ntwx=5000,
>> ntx=1, ntpr=100,
>> ntf=1, ntc=1, ntb=0,
>> igb=1, gbsa=0,
>> nsnb=25,
>> itgtmd=1, tgtmdfrc=10,
>> tgtfitmask=":1-674.CA,N,C,O",
>> tgtrmsmask=":1-674.CA,N,C,O",
>>
>> &end
>> &wt type='TGTRMSD', istep1=1, istep2=10000000, value1=2.00 , value2=0.0,
>> > &end
>>
>>
>> Any help will be really appreciated.
>>
>> with best regards
>>
>> Antonio
>>
>> --
>> Antonio Coluccia, Ph.D.
>> Department of Chemistry and Drugs Tecnology
>> La Sapienza University
>> Rome 00185
>> Piazzale Aldo Moro 5
>> antonio.coluccia.uniroma1.it
>> mobile: 00393406113351
>>
>>
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--
Antonio Coluccia, Ph.D.
Department of Chemistry and Drugs Tecnology
La Sapienza University
Rome 00185
Piazzale Aldo Moro 5
antonio.coluccia.uniroma1.it
mobile: 00393406113351
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Received on Mon Dec 22 2014 - 06:30:02 PST
