From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Fri Nov 30 2012 - 04:26:21 CST
Hi Jeff,
Yes you are right. In the CPU it works without a problem. It is a pity
since the GPU calculation for implicit solvent is really much faster.
Regards
Felipe
On 11/29/2012 11:57 PM, Jeff Wereszczynski wrote:
> Hi Felipe,
>
> Does it work properly with the CPU version? Or is it a problem with
> aMD+GB in general? I believe that the only aMD that works on the GPU
> is the dihedral acceleration (probably because those calculations are
> done on the CPU even in the GPU NAMD).
>
> Jeff
>
> On Thu, Nov 29, 2012 at 7:39 AM, Felipe Merino <fmerinoleon_at_gmail.com> wrote:
>> Dear all,
>>
>> I havwe been trying lately to run some accelerated molecular dynamics
>> combined with implicit solvent using a cuda version of NAMD 2.9. However,
>> when it comes to calculate the dV for the potential energy the
>> electrostatics are not calculated correctly.
>>
>> ACCELERATED MD: STEP 5000000 dV 174.884 dVAVG 174.884 BOND 217.271 ANGLE
>> 514.686 DIHED 785.12 IMPRP 0 ELECT -164.908 VDW -207.159 POTENTIAL 1145.01
>>
>> ETITLE: TS BOND ANGLE DIHED IMPRP
>> ELECT VDW BOUNDARY MISC KINETIC
>> TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
>>
>> ENERGY: 5000000 217.2714 514.6861 785.1195 0.0000
>> -3943.6178 -165.2773 0.0000 0.0000 813.3220
>> -1778.4960 309.5932 -2591.8180 -1768.8754 309.5932
>>
>>
>> I guess the program is not considering the solvation energy in the
>> calculation.
>>
>> Is there any way to correct this?
>>
>> Regards
>>
>> Felipe
>>
>
>
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