[gmx-users] error in equilibration

[Justin A. Lemkul]

Mark Abraham wrote:
>   On 9/02/2011 11:07 PM, shiva birgani wrote:
>> Dear Justin
>> I fallowed your tutorial of "Protein-Ligand Complex" to simulate a 
>> peptide associated with acetic acid. All the step was good but in 
>> Equilibration phase 1 I encountered with this error
>>
>> 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 Protein_A 1
>> turning all bonds into constraints...
>> Excluding 3 bonded neighbours for ACY 1
>> turning all bonds into constraints...
>> Excluding 2 bonded neighbours for SOL 6648
>> turning all bonds into constraints...
>> Excluding 1 bonded neighbours for NA+ 1
>> turning all bonds into constraints...
>> Excluding 1 bonded neighbours for CL- 0
>> turning all bonds into constraints...
>> NOTE:
>>   System has non-zero total charge: -9.999999e-01
>>

Mark's conclusion is correct.  The tutorial is for version 4.5.3, as stated in 
the introduction.  In addition, you should note here that you're not ready to 
equilibrate.  You've got a half-neutralized system, still with a -1 charge.

-Justin

>> processing coordinates...
>> double-checking input for internal consistency...
>> WARNING 2 [file "topol.top", line 1453]:
>>   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 261405
>> 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
>> -------------------------------------------------------
>>
>> how should I do correct it?
> 
> You're probably using a version of GROMACS that is years older than the 
> tutorial, and so will have minor compatibility issues. More recent 
> versions offer much better performance.
> 
> Mark
> 

-- 
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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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