[gmx-users] unit of surface tension, KJ/mol?

[Elisabeth]

On 22 March 2011 22:46, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Elisabeth wrote:
>
>
>>
>> On 22 March 2011 22:31, Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Elisabeth wrote:
>>
>>        Hello,
>>         I did two simulations on the same system using versions 4.0.7
>>        and 4.5.3. It seems like the unit of surface tension is not the
>>        same in these versions because I am getting ~250 KJ/mol an in
>>        4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted
>>        into bar nm? Can anyone help please.
>>
>>
>>    Is this from g_energy output?  In past versions, everything was
>>    printed as "kJ/mol," even quantities that obviously weren't, like
>>    temperature, pressure, etc.
>>
>>
>> Yes, so why are the results so different. I am using exactly the same mdp
>> file.!
>>
>>
> Any pressure-related quantity is going to be subject to enormous
> fluctuations. This has been discussed within the last few days.  Without
> seeing the .mdp file and a description of the system, it's hard for anyone
> to comment on what the results might mean.
>

Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is
extended in Z to create liq/air interface. That is 3X3X6 . What could be
reason for such a big difference in results from two version? Thanks alot!


integrator          =  md
dt                  =  0.002
nsteps              =  1000000

nstenergy           =  100
nstxout             =  100
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0
rlist               =  1.1
rcoulomb            =  1.1
rvdw                =  1.0

fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order          =  4
ewald_rtol          =  1e-5
;optimize_fft      =  yes

Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1
ref_t               =  300

pbc              =  xyz

gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

constraints             = all-bonds
constraint-algorithm = lincs


>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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