[gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/21/18 1:23 PM, negar habibzadeh wrote:
> hi . in vmd how can i find special number for each atom? i want to delete
> those atoms from my gro file.

You can label atoms by clicking on them in label mode. If you have 
further questions about VMD, post to their mailing list.

-Justin

> 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.
>>

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

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

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