[gmx-users] About negative values deuterium order parameters

[Justin Lemkul]

On 12/2/16 12:11 PM, Poncho Arvayo Zatarain wrote:
>
>
> Some days ago i send a quetion about negative values of deuterium order parameters in a 25% DPPC 75% DPPE+ nesthesic membrane. Thomas Piggot repond to me about the Scd que be negative too, specially for DPPC and DPPE. Now i send my obatained values for Scd. It is correct to have negative values? SN-1 and SN-3 correspond to DPPC and SN-2 and SN-4 correspond to DPPE. I watch the gro file in vmd and certainly look inclinable for the tails. All my other systems don´t have negative values like this one.
>
> Carbon  DPPC64+DPPE192+AN-SN1   DPPC64+DPPE192+AN-SN2   DPPC64+DPPE192+AN-SN3   DPPC64+DPPE192+AN-SN4
> 1       -0.207868       0.156621        -0.122543       0.202863
> 2       -0.199115       0.0507337       0.075788        0.0911758
> 3       -0.129733       0.0328502       0.0638192       0.0722099
> 4       0.159087        -0.0813808      0.0432806       0.0571403
> 5       -0.0940551      -0.0807225      -0.0842683      0.189616
> 6       -0.199373       -0.0259852      -0.0721477      0.167733
> 7       0.122858        -0.0486781      0.00461267      0.132131
> 8       0.135019        -0.0244167      -0.0931847      0.132473
> 9       0.134224        0.0127981       0.0474575       0.143573
> 10      0.135023        0.0502274       0.0901911       0.132179
> 11      0.128295        -0.0841136      0.0882197       0.0943604
> 12      0.125227        0.0756042       0.0349276       0.12459
> 13      0.115938        0.220139        -0.0766258      0.0861008
>

Something is clearly wrong.  You should have 14 values per lipid chain, not 13, 
and these numbers make no sense.  Make sure your index group is correct and gmx 
order is not emitting any warnings.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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