[gmx-users] why it is so slow

[Justin Lemkul]

On 11/2/12 10:56 AM, Albert wrote:
> 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)
>

I wasn't suggesting that you use NPT, I was merely pointing out that you made an 
statement that wasn't true and thought I would mention it.

It looks like you have other issues to deal with.

-Justin


-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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