[gmx-users] core dumped

[Justin Lemkul]

On 1/15/19 12:58 PM, rabee khorram wrote:
> Hello;
>
> Thank you Justin for your answer.
>
> I have mailed fe2o3.pdb file in this gmail for you.

The mailing list does not accept attachments, nor would a PDB file be 
useful here.

>    in atomname2type.n2t, for Fe-O bonds, I have used Fe type From the
> atomtype.atp of charmm36 force field,
>
> :   (FE  55.84700 ;     heme iron 56)
>
>    is it correct?

The CHARMM Fe atom type has only been parametrized for heme. I have no 
idea if it will be suitable for any other system. Likely not. Charge 
assignment is also non-trivial for a system like this.

-Justin

>
>
>
> On Tue, Jan 15, 2019 at 5:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/15/19 6:47 AM, rabee khorram wrote:
>>> Segmentation fault (core dumped)?
>>> *Hello everyone, I am runnig nano Fe2O3 structure with PEN drug with
>>> gromacs5.*
>> How did you parametrize and validate these species?
>>
>>> *but in step :*
>>>
>>> * gmx mdrun -v -deffnm nvt *
>>>
>>> * I am getting an error : step 2600, remaining wall clock time: 60 s
>>> Segmentation fault (core dumped)*
>>>
>>> *and don't create nvt.gro.!*
>>>
>>> *can you explain to me what is my problem?*
>>> *thank you very much.*
>> http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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