[gmx-users] links warnangles

[Dimitris Dellis]

Hi.
There is an issue with constraints.
H atom position is not uniquely defined with the constraints you use.
Try these constraints (substitute symbols with numbers)

1       2    1       rC-H
1       3    1       rC-CL
1       4    1       rC-CL
1       5    1       rC-CL
2       3    1       rH-CL
2       4    1       rH-CL
3       4    1       rCL-CL
3       5    1       rCL-CL
4       5    1       rCL-CL

DD


On 02/02/2011 06:20 PM, vferrario at units.it wrote:
> The dynamic works, but I still have the same problems with 
> minimization...
>
>
> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>
>>
>>
>> vferrario at units.it wrote:
>>> Ok and which definition have you used? the previous one with 5 atom 
>>> for molecule?
>>>
>>
>> Yes.
>>
>> -Justin
>>
>>> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>>>
>>>>
>>>>
>>>> vferrario at units.it wrote:
>>>>> Just the last thing... can you copy your mdp file? I think I'm 
>>>>> having some problems also with that... Thanks.
>>>>>
>>>>
>>>> For EM, I used the .mdp file you posted in your first message and 
>>>> added the line "continuation = yes."  For MD, I changed nstlist 
>>>> from 100 to 5.
>>>>
>>>> -Justin
>>>>
>>>>> Valerio
>>>>>
>>>>>
>>>>> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>>>>>
>>>>>>
>>>>>>
>>>>>> Justin A. Lemkul wrote:
>>>>>>
>>>>>> <snip>
>>>>>>
>>>>>>> I've obtained a stable trajectory for a single CHCL3 molecule.  
>>>>>>> By setting "continuation = no" (so that constraints are not 
>>>>>>> solved before step 0) in the em.mdp file, and then reducing 
>>>>>>> nstlist to 5 in md.mdp, I
>>>>>>
>>>>>> Ack, this should be "continuation = yes."  Sorry for the 
>>>>>> confusion.  I will copy from my .mdp file...I will copy from my 
>>>>>> .mdp file... :)
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> -- 
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>> -- 
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at 
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>
>>>>>
>>>>>
>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> -- 
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at 
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>>
>>>
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110202/b26ab1f6/attachment.html>