[gmx-users] KALP15 in DPPC

[negar habibzadeh]

hi . in vmd how can i find special number for each atom? i want to delete
those atoms from my gro file.
tnx


On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>
>> tnx so much
>>   i got nvt.tpr and now i want to run it but i am getting this error :
>> Fatal error:
>> Too many LINCS warnings (5258)
>> 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
>>
>> I use position restraints on the lipid headgroups for P of DOPC . i add
>> the
>> following lines to the system topology after the #include "dopc.itp" line.
>>
>> #include "DOPC.itp"
>>
>> #ifdef POSRES_LIPID
>> #include "lipid_posre.itp"
>> #endif
>>
>> and i add the following line in nvt.mdp :
>> define          = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
>> for each protein and for DOPC P
>>
>> i created lipid_posre.itp :
>>
>> ; position restraint file for DOPC P
>>
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>     20    1       0       0       1000
>> ~
>>
>> i used position restraints for lipids but again when i want to run nvt  ,i
>> get this error :
>>
>> Fatal error:
>> Too many LINCS warnings (5258)
>> 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
>>
>> how can i solve this problem ?
>>
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System
>
> -Justin
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> 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.
>