[gmx-users] Hello Regarding Lincs error

[RINU KHATTRI]

hello justin
yes i did minimization and equilibrium
i have one confusion when i am going for extension of simulation by
tpbconv -s md_0_1.tpr -extend 9000 -o nextr.tpr
for mdrun i have to use which checkpoint file md_0_1.cpt after 1 ns or
state.cpt i am always confused with it i am usin 4.5.5 so append is
default still the outputfile of 1st run is not appended
just backoff traj,trr to #traj.trr.1#
mdrun   -s nextr.tpr -cpi state.cpt
or mdrun -s nextr -cpi md_0_1.cpt
kindly help


On Thu, Sep 18, 2014 at 5:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/18/14 6:38 AM, RINU KHATTRI wrote:
>>
>> hello
>> i am also facing the same problem i worked on the protein complex
>> (popc ) but once again i am using same procedure its gives error even
>> i changed .mdp file parameters
>
>
> Changed to what?  From what?
>
>> after running it gives 61%
>> mdrun
>>
>> grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o
>> npt.tpr
>>
>>   mdrun -nt 4 -deffnm npt
>
>
> Did previous minimization and/or equilibration runs succeed?
>
> -Justin
>
>
>> kindly help
>>
>> On Thu, Sep 18, 2014 at 2:23 PM, Ujwala Patil <ujwalanpatil at gmail.com>
>> wrote:
>>>
>>> Hello I am doing simulation of   dioxane+ water system
>>> during energy minimization i got error
>>> Too many LINCS warnings (1337)
>>> If you know what you are doing you can adjust the lincs warning threshold
>>> in your mdp file
>>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>>> but normally it is better to fix the problem
>>>
>>> my em.mdp file is
>>>
>>> integrator  = steep      ;
>>> emtol       = 500.0
>>> emstep      = 0.01
>>> nsteps      = 500
>>>
>>> nstlist     = 1.4
>>> ns_type     = grid
>>> rlist       = 1.0
>>> coulombtype = PME
>>> rcoulomb    = 1.0
>>> rvdw        = 1.4
>>> constraints = none
>>> pbc         = xyz
>>>
>>>
>>> i have  seen some  similar type of error
>>>
>>> but not able to fix
>>>
>>> please help me to solve the problem
>>> --
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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 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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