[gmx-users] regarding NVT

[Justin A. Lemkul]

priya thiyagarajan wrote:
> hello sir,
> Thanks for your reply
> 
> initially i tried with v-rescale i am getting error..
> now again i tried ..
> when i tried my NVT by changing tcouple=V-rescale
> i am getting the following error..
> 
> 
> 
> creating statusfile for 1 node...
> *ERROR: invalid enum 'V-rescale' for variable tcoupl, using 'No'*
> Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 
> 'Andersen-interval'
> WARNING 1 [file nvt.mdp, line unknown]:
>   Unknown left-hand 'continuation' in parameter file
> 
> checking input for internal consistency...
> calling cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for DRG 20
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 32095
> turning all bonds into constraints...
> NOTE:
>   System has non-zero total charge: -6.000000e+01
> 

Your system has a net charge of -60, indicating that it is likely not 
constructed correctly.

> processing coordinates...
> double-checking input for internal consistency...
> WARNING 2 [file "topol.top", line 44]:
>   For energy conservation with LINCS, lincs_iter should be 2 or larger.
>   You can safely ignore this if your system doesn't have any
>   LINCS-constrained bonds;
>   for water molecules we normally use the analytical SETTLE algorithm
>   instead.
> Setting gen_seed to 952010
> Velocities were taken from a Maxwell distribution at 300 K
> 
> There were 2 warnings
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 1132
> 
> Fatal error:
> There were 1 error(s) processing your input
> -------------------------------------------------------
> 

Upgrade to a more modern version of Gromacs (i.e. 4.5.5) and try again.  There 
is no reason to use software that is several years old.

-Justin

> 
> 
> 
> 
> 
> please help me with your answer..
> 
> 
> Thanking you
> 

-- 
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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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