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shylishyli 

Materials studio -- Rigid body atoms are shared, or related by symmetry or periodicity.

Hi,

I am trying to use COMPASS in Forcite to optimize a crystal structure. I choose to keep motion groups rigid. However it fails:
Rigid body atoms are shared, or related by symmetry or periodicity.

How can I fix this problem? Thank you!

Shuying
CarstenCarsten (Accelrys) 
One remark at the beginning: the seedname.stp file is just a file which contains some info about the project but no structures most of the things are in the seendname_Files folder and they always go together.

Could you please close the relevant *.xsd file and zip and post it?

Please double check that no atom is part of two motion groups.

In crystals it sometimes happens that symmetry images are assigned to multiple motion groups.
Please deleted all defined motion groups which are defined twice.

Which Materials Studio version do you use?
shylishyli
Hi, 

I am using MS 2016. I checked and could not find any atoms belonging to 2 groups. I also tried to assiagn motion groups manually but still got the same problem.

Thank you!
Shuying
Felix HankeFelix Hanke
Hi,
What is the symmetry of the crystal? If it is any higher than P1 then you may get this problem because molecules are related to each other by symmetry: move one and you'll also affect the other to keep symmetry intact. 
What happens when you try Build | Symmetry | Make P1 before starting the MD simulation?
Best, 
Felix
 
shylishyli

Hi,

This makes sense. However if I erase the symmetry and allow changes in unit cell parameter, the structure will change a lot, which is not what I expected. How can I solve this problem?

Thanks a lot!

Shuying

CarstenCarsten (Accelrys) 
Where does the structure come from?

What happens if you define the atoms of the organic system in the asymmetric unit as motion group?

One problem I see is that COMPASS does not have parameters for I unless it is I-.
Jason DeJoannisJason DeJoannis
Hi Shuying,
 
I think COMPASS may be having trouble with the sulfur atoms. First of all, I notice the system has a net charge of -4. Shouldn’t the net charge be zero for any crystal structure? So the sulfurs must have a positive charge to compensate. The -S-S- moiety coming off the aromatic rings is unusual. You should check into the chemistry of that. Once you are sure you have the right chemistry, perhaps a next step is to try some DFT calculations both in the crystal and in the gas phase. That can be used to validate whether the forcefield is reasonable.

Best,
Jason
CarstenCarsten (Accelrys) 
The -4 charge come from the Iodine centers and which I assume are not I- as assigned by COMPASS and COMPASSII.
shylishyli

Thanks Jason and Carsten!

I downloaded the structure from CCDC. So COMPASS does not assign correct charges and I need to assign manually, right?

shylishyli

Thanks Jason and Carsten!

I downloaded the structure from CCDC. So COMPASS does not assign correct charges and I need to assign manually, right?

CarstenCarsten (Accelrys) 
  1. Manually, calculate the forcefield types for the molecule (under Forcite_Calculation->Energy->Forcefield->More... calculate the Forcefield types)
  2. Use Calculate forcefield assigned charges to calculate the charges.
  3. Change the settings for the charges to "Use Current"
  4. Use Modify->Charges->Edit to assign a charge of 0 to the I- force field types.

I suggest to double check how accurate the original structure really was measured.