[gmx-users] Hello Regarding Lincs error

[Justin Lemkul]

On 9/22/14 1:23 AM, RINU KHATTRI wrote:
> 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
>

I have no idea.  How did you name your files?  Do state.cpt and md_0_1.cpt 
co-exist?  What is in them?  If you ran a 1-ns simulation with mdrun -deffnm 
md_0_1, then you extend using md_0_1.cpt.  This is why I always name my files 
descriptively or organize different parts of a simulation (equilibration, 
production intervals, etc) in different directories.

-Justin

>
> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>
>>
>> --
>> ==================================================
>>
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
>> mail to gmx-users-request at gromacs.org.

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================