AMBER Archive (2008)

Subject: Re: AMBER: interaction energies in Amber and VMD/NAMD

From: Alan (alanwilter_at_gmail.com)
Date: Tue Jul 29 2008 - 03:19:16 CDT

Looking only at the figure, it seems there's a factor of 2x in amber
vdw x namd vdw. I really don't know which one is correct and I don't
know how Namd plugin is working.

However you said you didn't put 1-4vdw term in your program, right?
Well, I would say that it would do a good difference in your results.

Is it possible for your to send me a spreadsheet with vdw values from
amber and namd?

Have you tried with switching 'on'?

Sorry for asking again because I may missing something else here: so
your ran a simulation in sander and namd2 right? and now you are
trying to compare ele and vdw results, right?

Which traj files are you trying with VMD NAMDEnergy? AFAIK VMD can
read sander traj files and you can see results with NAMDEnergy. Are
you trying to compare sander x namd2 or just checking if your program
is working fine for sander as NAMDEnergy seems to work for namd2?

Cheers,
Alan

On Mon, Jul 28, 2008 at 1:38 AM, Alessandro Nascimento
<al.s.nascimento_at_gmail.com> wrote:
> Thanks, David, Carlos and Alan.
>
> I am attaching a picture showing how different the results are.
>
> These results were from a simulation of a waterbox (TIP3P) using
> sander. I choose a waterbox to debug the contribution of the 1-4vdw
> term (which is missing so far in my simple code).
>
> The system was setup using leap as follows:
>
> wat = createunit wat
> solvatebox water TIP3PBOX 12.0
>
> Then I minimized the system in sander, and ran a productive run
> (100000 steps) also in sander, turning ntb=0.
>
> So far, I ve being defining vdw as :
>
> iaci = Natomtypes*(iac[i]-1);
> ic = ico[(iaci+iac[j])-1]; // the `-1` corrects
> for the array index which start in 0 rather than 1
> if (ic > 0) {
> vdw = vdw + (((LJA[ic-1])/(r2*r2*r2*r2*r2*r2))-((LJB[ic])/(r2*r2*r2))); }
> else {
> vdw = vdw +
> (((LJA[ic-1])/(r2*r2*r2*r2*r2*r2))-((LJB[ic])/(r2*r2*r2*r2*r2))); }
>
> Using vmd to compute the interaction energy between molecule 1 and the
> other ones (using the parameters suggested in the namd manual for
> amber ff simulations:
>
> switching off
> exclude 1-4scaling
> 1-4scaling 0.83333
> cutoff 35.0
>
> gives the results I show you in the picture
>
> Any idea of what I may be missing?
>
> Thanks a lot,
>
> --alessandro
>
>
>
> On Sat, Jul 26, 2008 at 11:26 PM, Alan <alanwilter_at_gmail.com> wrote:
>> Alessandro,
>>
>> Have you looked at http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html?
>>
>> Pay well attention to:
>>
>> 3. NAMD has several exclusion policy options, defined by exclude. The
>> way AMBER dealing with exclusions corresponds to the ``scaled1-4'' in
>> NAMD. So for simulations using AMBER force field, one would specify
>> ``exclude scaled1-4'' in the configuration file, and set 1-4scaling to
>> the inverse value of SCEE as would be used in AMBER.
>>
>> 5. By default, NAMD applies switching functions to the non-bond
>> interactions within the cutoff distance, which helps to improve energy
>> conservation, while AMBER does not use switching functions so it
>> simply truncates the interactions at cutoff. However, if ``authentic''
>> AMBER cutoff simulations are desired, the switching functions could be
>> turned off by specifying ``switching off'' in NAMD configuration file.
>>
>> and check those parameters in your namd.conf file:
>> 1-4scaling 0.833333 # =1/1.2, default is 1.0
>> scnb 2 # This is default
>> switching off # Turn off the switching functions, try on also
>> readexclusions yes #you may compare with 'no' too.
>>
>> And , as David ask, how much is the difference in percentage?
>>
>> Cheers,
>> Alan
>>
>> On Sun, Jul 27, 2008 at 1:46 AM, Carlos Simmerling
>> <carlos.simmerling_at_gmail.com> wrote:
>>> I don't think Alessandro used Amber for energies, and if it's a simple program
>>> it probably is non-periodic. I think it's likely the 1-4 scaling factor for vdw.
>>> one of them ( can't recall, Adrian may know) either ele or vdw has the
>>> wrong 1-4 scaling in NAMD for amber ff.
>>>
>>> On Sat, Jul 26, 2008 at 8:36 PM, David A. Case <case_at_scripps.edu> wrote:
>>>> On Sat, Jul 26, 2008, Alessandro Nascimento wrote:
>>>>>
>>>>> I wrote a simple program to read some information in the prmtop file
>>>>> and compute nonbonded energies (ele+vdw) from a sander/pmemd
>>>>> trajectory and I am trying now to compare my first test results with
>>>>> the ones from the plugin NAMDEnergy in VMD. For electrostatic
>>>>> computation, they match perfectly. For vdw, however, seems like
>>>>> vmd/namd overestimates the energetic contribution. Does anyone has any
>>>>> experience on comparing results between amber and vmd/namd ?
>>>>
>>>> I don't have experience, but as a guess: Amber by default includes a
>>>> correction for vdw interactions beyond the cutoff; NAMD might not inlcude
>>>> such a term. How different are the results?
>>>>
>>>> ...dac
>>>>
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>>>
>>>
>>>
>>> --
>>> ===================================================================
>>> Carlos L. Simmerling, Ph.D.
>>> Associate Professor Phone: (631) 632-1336
>>> Center for Structural Biology Fax: (631) 632-1555
>>> CMM Bldg, Room G80
>>> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>>> ===================================================================
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>>
>>
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>>http://www.bio.cam.ac.uk/~awd28<<
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>
>
>
> --
> [ ]s
>
> --alessandro
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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