[gmx-users] 3.3beta vs 3.2 dispersion correction term

[Sukit Leekumjorn]

Hi David,

Just to make sure that I did not do anything wrong, I tried using a 
lipid system of 35840 atoms (below the limit listed in the 
feature/changes website, 46340 atoms ) .  Using the same mdp file, pme 
with correction factor, below is the result of step 0. The results came 
out to be almost exactly the same in all 4 cases and I am certain that I 
did the same procedures as before. Can you please describe in detail on 
how you obtained a total energy -1.73585e+06 (Disp corr -3.54849e+04) 
from gmx benchmark system.

Thank you for your help

Sukit

Cutoff 3.2.1
Total energy = -4.61915e+5

PME 3.2.1
Disper. corr. = -9.32428e+3
Total energy = -4.70591e+5

Cutoff 3.3.B
Total energy = -4.61912e+5

PME 3.3.B
Disper. corr. = -9.32271e+3
Total energy = -4.70812e+5

David wrote:

>On Thu, 2005-07-28 at 10:38 -0400, Sukit Leekumjorn wrote:
>  
>
>>Thank your for your reply, David
>>
>>I downloaded the beta version on July 8 2005 from the CVS usage 
>>website.  I noticed that the heading of the program is in VERSION 
>>3.3_beta_20050202. I am not certain if this is the latest version. If it 
>>is not, can you please let me know the patches for the latest version.
>>
>>    
>>
>if you used CVS then you can get later patches by typing 
>cvs update
>I'm afraid that doesn't explain it however.
>
>  
>
>>Sukit
>>
>>David wrote:
>>
>>    
>>
>>>On Wed, 2005-07-27 at 16:58 -0400, Sukit Leekumjorn wrote:
>>> 
>>>
>>>      
>>>
>>>>Thank you for your reply, David
>>>>
>>>>Sorry about not comparing things one at a time.  I took your suggestion 
>>>>and tried comparing both cutoff (rvdw=1 and rcoulomb=1.8) and pme 
>>>>(rvdw=0.9 and rcoulomb=0.9) for both versions without corrections; and 
>>>>it turns out to be almost exactly the same. I then took an additional 
>>>>step to compare the pme simulation including the correction factor for 
>>>>both versions.  Listed below is the total energy caculated in step 0.  
>>>>You mentioned that the corrction factor in 3.2.1 version is not correct 
>>>>and it is fixed in the 3.3B version, I am not sure if this is normal for 
>>>>the correction factor to be 2 orders of magnitude higher, which greatly 
>>>>effects the total energy of the system.
>>>>
>>>>3.2.1 cutoff: -1.71612e+6
>>>>3.2.1 pme without correction: -1.69195e+6
>>>>3.2.1 pme with correction: -1.69664e+6 (Disp Corr = -4.69360e+3)
>>>>
>>>>3.3B cutoff: -1.71385e+6
>>>>3.3B pme without correction: -1.69413e+6
>>>>3.3B pme with correction: -1.96249e+6 (Disp Corr = -2.68357e+5)
>>>>   
>>>>
>>>>        
>>>>
>>>I get different numbers (step 0 only):
>>>PME with correction Total energy -1.73585e+06  (Disp corr  -3.54849e+04)
>>>
>>>Are you sure you have the latest version? There have been changes in
>>>this code in april, see:
>>>http://www.gromacs.org/features/changes33.html
>>> 
>>>
>>>      
>>>
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