Hi,
I agree with your comment. I think what puzzles me is the scmask keyword. For example if I use scmask='x,y' for state 0 and scmask='x' for state 1, or use scmask='y' for state 0 and scmask=' ' for state 1, assuming everything else is the same, am I going to get the same dv/dl for each transformation step?
Best,
Lishan
----- Original Message -----
From: <steinbrt.rci.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, May 06, 2011 3:28 PM
Subject: Re: [AMBER] question about scmask
> Hi,
>
> are the total free energy changes different? The result from one
> transformation substep cannot easily be compared to that of some other
> one, only results from complete thermodynamic cycles are physically
> interpretable. For example, since you have removed different charge sets
> in the first step of the two cases, you will get different distributions
> of water around the molecules for the vdw steps, leading to different
> deltaGs (different, but not necessarily wrong in either case).
>
> If doing the complete transformation twice along different routes (i.e.
> with different scmasks) gives very different results, then something is
> indeed wrong, but you cannot know that just from partial results of the
> substeps.
>
> That said, if your substep results differ enourmously, by say 100kcal/mol,
> then something is clearly wrong...
>
> Thomas
>
> On Thu, May 5, 2011 8:53 pm, Lishan Yao wrote:
>> Hi,
>>
>> Thank you for the response. I think what makes me confused is the scmask
>> keyword. In the first case,
>> scmask=':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>> scmask=':3.CB,HB1,HB2,HB3' for GAG
>> my understanding is that the atoms including
>> ':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' are decoupled with softcore method
>> from the surroundings while the atoms including scmask=':3.CB,HB1,HB2,HB3'
>> are coupled to the surroundings.
>> In the second case,
>> scmask=':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>> scmask=':3.HB1,HB2,HB3' for GAG
>> atoms including ':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' are decoupled with
>> softcore method from the surroundings while the atoms including
>> scmask=':3.HB1,HB2,HB3' are coupled to the surroundings. If my
>> understanding is correct, I would expect the same deltaG values from one
>> transformation since the initial and final state are the same for both
>> cases (CB is a common atom in GTG and GAG, I would think it doesn't matter
>> if I exclude it from scmask).
>>
>> Best,
>> Lishan
>>
>>
>>
>> ----- Original Message -----
>> From: <steinbrt.rci.rutgers.edu>
>> To: "AMBER Mailing List" <amber.ambermd.org>
>> Sent: Thursday, May 05, 2011 6:33 PM
>> Subject: Re: [AMBER] question about scmask
>>
>>
>>> Hi,
>>>
>>> two things:
>>>
>>> a) Are you talking about deltaG values from one transformation? These
>>> will
>>> certainly be different. Only deltadeltaG values from a properly set up
>>> thermodynamic cycle will give interpretable results.
>>>
>>> b) If you do get very different ddG values, this indicates that your
>>> simulation is not converged. You don't give simulation details, so it's
>>> impossible to judge that.
>>>
>>> Kind Regards,
>>>
>>> Thomas
>>>
>>> On Thu, May 5, 2011 5:29 am, Lishan Yao wrote:
>>>> Dear Amber users,
>>>>
>>>> I set up a alchemy simulation for the GTG to GAG mutation in water
>>>> (with head and tail groups neutralized). Following the typical
>>>> procedure, I did electrostatics first and then vdw. In the vdw alchemy
>>>> process, I used softcore method. But I got very different dv/dl values
>>>> when I use
>>>>
>>>> scmask=':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>>>> scmask=':3.CB,HB1,HB2,HB3' for GAG
>>>> or
>>>> scmask=':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>>>> scmask=':3.HB1,HB2,HB3' for GAG
>>>>
>>>> I can't figure out what is the problem. It seems to me they should give
>>>> same or at least similar results.
>>>>
>>>> Best,
>>>> Lishan
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> Dr. Thomas Steinbrecher
>>> formerly at the
>>> BioMaps Institute
>>> Rutgers University
>>> 610 Taylor Rd.
>>> Piscataway, NJ 08854
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>> _______________________________________________
>> AMBER mailing list
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>>
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri May 06 2011 - 01:30:03 PDT
