Rahul,
can you send me directly (off the amber list) your inputs so I can do
a bit of debugging? better to try on your actual system.
carlos
On Fri, Apr 8, 2011 at 2:31 PM, Rahul Banerjee
<rahul.banerjee.chemistry.msu.edu> wrote:
> Yes my tgtrmsmask contains 953 atoms. Stated below is the way I have defined the mask:
> tgtfitmask=":1-120.CA",
> tgtrmsmask=":1-120&!.H="
>
> The output says:
> Mask ":1-120.CA" matches 120 atoms
> Mask ":1-120&!.H=" matches 953 atoms
>
> If you back calculate the number of atoms in the mask from Restraint energy they will be 931 and 947 respectively (they must be the same!!). I am using TGTMDFRC as 2.
>
> Thanks for your input and suggestions.
>
> With best regards,
> Rahul Banerjee
> ________________________________________
> From: Carlos Simmerling [carlos.simmerling.gmail.com]
> Sent: Friday, April 08, 2011 2:06 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Restraint potential in Targeted MD
>
> the code matches what you wrote. are you sure that is the correct #
> atoms in the mask? check the sander output and see what is says for
> each of your masks.
>
>
> On Fri, Apr 8, 2011 at 1:56 PM, Rahul Banerjee
> <rahul.banerjee.chemistry.msu.edu> wrote:
>> Dear Amber users,
>>
>> I was doing TMD simulation for a small protein of 120 amino acids. The force constant (TGRMDFRC) I was using is 2. I was applying restrain force on all the heavy atoms (NTTGTRMS = 953) but aligning the structure with the reference structure based on their C* trace (120 C* atoms). I was trying to calculate the Restrain potential from the following equation in the Amber10 manual:
>>
>>
>>
>> E = 0.5 * TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2
>>
>>
>> If I calculate the restraint energy (RESTRAINT) for the given example and they come out to be slightly different (1.3761 and 2.0165 compared to 1.3443 and 2.0047 respectively). I have considered RMSD as "Current RMSD from reference" and TGTRMSD as "Current target RMSD" (please see the example below). Why there is such deviation? I guess it is not truncation error or something like that.
>>
>> Thank you for your input.
>>
>> With best regards,
>> Rahul Banerjee
>>
>> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>> ===============================================================================
>> NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 281.47 PRESS = 78.8
>> Etot = -59693.3975 EKtot = 13225.6527 EPtot = -72919.0502
>> BOND = 344.6748 ANGLE = 917.0819 DIHED = 1246.7549
>> 1-4 NB = 437.6376 1-4 EEL = 6023.0834 VDWAALS = 9689.5997
>> EELEC = -91579.2268 EHBOND = 0.0000 RESTRAINT = 1.3443
>> EAMBER (non-restraint) = -72920.3945
>> EKCMT = 5952.4662 VIRIAL = 5561.2691 VOLUME = 229880.0226
>> Density = 1.0182
>> Ewald error estimate: 0.7172E-04
>> Current RMSD from reference: 0.788
>> Current target RMSD: 0.750
>> ------------------------------------------------------------------------------
>> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>> ===============================================================================
>> NSTEP = 150 TIME(PS) = 0.300 TEMP(K) = 294.87 PRESS = 118.7
>> Etot = -58177.1508 EKtot = 13855.3267 EPtot = -72032.4775
>> BOND = 367.8662 ANGLE = 962.7299 DIHED = 1283.7928
>> 1-4 NB = 447.1210 1-4 EEL = 6022.8517 VDWAALS = 9476.6759
>> EELEC = -90595.5197 EHBOND = 0.0000 RESTRAINT = 2.0047
>> EAMBER (non-restraint) = -72034.4822
>> EKCMT = 6235.2483 VIRIAL = 5646.1869 VOLUME = 229936.7782
>> Density = 1.0179
>> Ewald error estimate: 0.6539E-05
>> Current RMSD from reference: 0.796
>> Current target RMSD: 0.750
>>
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>>
>
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Received on Fri Apr 08 2011 - 12:00:09 PDT
