On 10/8/16 2:58 AM, Sameer Edirisinghe wrote:
Dear gromacs users, Dr. Justin,
I managed to run md simulation with the aid of your helps here . As the
next step I'm trying to create a crystal from polymer molecule so i can put
several molecules to the same box and do a simulation. What
Dear gromacs users, Dr. Justin,
I managed to run md simulation with the aid of your helps here . As the
next step I'm trying to create a crystal from polymer molecule so i can put
several molecules to the same box and do a simulation. What approach should
I take here ?
Regards
Sameera
On 9/21/16 7:42 AM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
Thanks for the explanation. Now i got the point you mentioned here. Then i
checked the bonds i have mentioned in .rtp file and then i found the
relevant bonded type. then i checked the ffbonded.itp file and i found that
bond type
Dear Dr. Justin,
Thanks for the explanation. Now i got the point you mentioned here. Then i
checked the bonds i have mentioned in .rtp file and then i found the
relevant bonded type. then i checked the ffbonded.itp file and i found that
bond type is already in there.
As an example,
CAY HA1 ;
On 9/20/16 8:27 AM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
Thanks for the all valuable points here. Please see the below sample bonds
i defined in .rtp file. how to define bond type for them ? i know oplsaa
atom type of each of them. what i dont understand in how to add them to
Dear Dr. Justin,
Thanks for the all valuable points here. Please see the below sample bonds
i defined in .rtp file. how to define bond type for them ? i know oplsaa
atom type of each of them. what i dont understand in how to add them to
ffbonded.itp file. these bonds are general bonds such as C-C
On 9/18/16 10:14 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
If the bond types have not added, following errors occuring with grompp,
1) ERROR 1 [file topol.top, line 108]:
No default Bond types
2) ERROR 2 [file topol.top, line 168]:
No default Angle types
3) ERROR 3 [file
Dear Dr. Justin,
If the bond types have not added, following errors occuring with grompp,
1) ERROR 1 [file topol.top, line 108]:
No default Bond types
2) ERROR 2 [file topol.top, line 168]:
No default Angle types
3) ERROR 3 [file topol.top, line 426]:
No default Ryckaert-Bell. types
On 9/18/16 2:26 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
Now i can understand what what i have mistaken there. How can i derive
[bondtypes]
for bonds i have used in .rtp file ?
Determine if you need to in the first place. If grompp gives you errors about
missing parameters, first
Dear Dr. Justin,
Now i can understand what what i have mistaken there. How can i derive
[bondtypes]
for bonds i have used in .rtp file ?
Regards
On Sun, Sep 18, 2016 at 11:38 PM, Justin Lemkul wrote:
>
>
> On 9/18/16 2:06 PM, Sameer Edirisinghe wrote:
>
>> Dear Dr. Justin,
On 9/18/16 2:06 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
If atom names names cant use in ffbonded.itp file how should i add bond
interaction used in .rtp file to ff..itp file ? this is the part i dont
understand. Do i need to modify ffnonbonded.itp file to correct the "Unknown
Dear Dr. Justin,
If atom names names cant use in ffbonded.itp file how should i add bond
interaction used in .rtp file to ff..itp file ? this is the part i dont
understand. Do i need to modify ffnonbonded.itp file to correct the "Unknown
bond_atomtype' error which occurring while runing grompp
On 9/18/16 1:12 PM, Sameer Edirisinghe wrote:
Dear Dr. Justin,
Thanks for the reply. Following is the whole .rtp file i used. ( As you
said it was generated by using PRODRG)
You shouldn't use the charges from PRODRG. They assume a united-atom force
field, and are of very low quality.
On 9/18/16 12:30 PM, Sameer Edirisinghe wrote:
Dear users,
There is one thing i cannot clarify from gromacs manual which is about
following error occurred while running grompp
Fatal error:
Unknown bond_atomtype CAY
I used to create .rtp file from atom types which are already defined in
Dear users,
There is one thing i cannot clarify from gromacs manual which is about
following error occurred while running grompp
Fatal error:
Unknown bond_atomtype CAY
I used to create .rtp file from atom types which are already defined in
atomtype.atp file. But still above error occurring
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