[gmx-users] Martini force field - coarse grained protein tutorials

[Justin Lemkul]

On 10/2/14 1:39 PM, David Ackerman wrote:
> Hello,
>
> I am also attempting to run Martini using version 5 and am getting the same
> two errors with an mdp file that worked (aside from warnings) on version
> 4.6.5. Does anyone have a solution to this problem?
>

It's because the default cutoff scheme has changed.  Since the .mdp file does 
not specify a cutoff-scheme, grompp assumes Verlet, so the options given in the 
.mdp file trigger errors.  If you specify "cutoff-scheme = group" or otherwise 
change the settings to be compatible with Verlet, grompp should work.  The 
equivalent options under Verlet are all described on manual.gromacs.org and in 
the PDF manual.

-Justin

> On Mon, Sep 15, 2014 at 3:37 AM, Sridhar Kumar Kannam <srisriphy at gmail.com>
> wrote:
>
>> Hi Tsjerk,
>>
>> Thank you. I missed those links.
>>
>> Now when I minimize the system (protein in vacuum) I am getting the
>> following errors. I am using 5.0 version.
>>
>> ERROR 1 [file minimization-vaccum.mdp]:
>>    With Verlet lists only cut-off, reaction-field, PME and Ewald
>>    electrostatics are supported
>>
>> ERROR 2 [file minimization-vaccum.mdp]:
>>    Explicit switch/shift coulomb interactions cannot be used in combination
>>    with a secondary coulomb-modifier.
>>
>>
>> Can you please explain them ...
>>
>>
>> Thanks again.
>>
>>
>>
>>
>>
>>
>> On Mon, Sep 15, 2014 at 5:23 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> wrote:
>>
>>> Hi Sridhar,
>>>
>>> Have you tried clicking on the .mdp file names in the commands, which are
>>> underlined and highlighted in blue? Seems to work for me.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>> On Sep 14, 2014 12:41 PM, "Sridhar Kumar Kannam" <srisriphy at gmail.com>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I am a newbie to Gromacs and Martini force field. I begin with the
>>>> tutorials - http://md.chem.rug.nl/cgmartini/index.php/proteins
>>>>
>>>> As this tutorial does not provide the .mdp files I have tried to built
>>> the
>>>> .mdp files based on other Gromacs tutorials. But when I run the
>>> simulations
>>>> I am getting different kinds of error. As I have not read the manual
>> yet,
>>>> its hard to debug the errors. Can someone please share the *mdp files
>> to
>>>> run this tutorial (Ubiquitin and HIV-Prtease) simulations.
>>>>
>>>> Thank you.
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Cheers !!!
>>>> Sridhar  Kumar Kannam :)
>>>> --
>>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Cheers !!!
>> Sridhar  Kumar Kannam :)
>> --
>> Gromacs Users mailing list
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================