[gmx-users] core dumped

[rabee khorram]

Thank you very much Justin.

Sent from my iPhone

> On Jan 17, 2019, at 1:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> 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
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>>> 
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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
> 
> ==================================================
> 
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