[gmx-users] why it is so slow

[Albert]

On 11/01/2012 06:15 PM, Justin Lemkul wrote:
>
>
> On 11/1/12 12:55 PM, Albert wrote:
>> hello:
>>
>>   I am running a 40ns REMD with GBSA solvent NPT simulations. It is 
>> exchange for
>> 16 different temperature with exchange step 300.
>>
>
> Based on your .mdp file, you're not doing NPT (pcoupl = no). 

Hello Justin:

thanks a lot for kind reply.

If I turn this option on, such as:

  pcouple=Isotropic

it is said:


ERROR 1 [file eq.mdp, line 78]:
   Pressure coupling not enough values (I need 1)


WARNING 1 [file eq.mdp]:
   Turning off pressure coupling for vacuum system

Setting the LD random seed to 14221350

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: gmxcpp.c, line: 248

Fatal error:
Topology include file "ligand.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Cowardly refusing to create an empty archive" (GNU tar)