[gmx-users] Re: Umbrella Sampling settings

[Justin Lemkul]

On 7/12/13 2:28 PM, Shima Arasteh wrote:
> Thanks for your replies. :-)
> So, if I want to the ion move in only z-direction, I need to set the 'pull_dim' Y Y N? Correct?
>
> But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the z-dimension.  Thus, x and y are set to "no" (N) and z is set to "yes" (Y).
>
> So what should I do?!
>

The pull_dim setting is irrelevant when using position geometry.  Only pull_vec1 
matters here.

-Justin

>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Thomas Schlesier <schlesi at uni-mainz.de>
> To: gmx-users at gromacs.org
> Cc:
> Sent: Friday, July 12, 2013 9:04 PM
> Subject: [gmx-users] Re: Umbrella Sampling settings
>
> In GROMACS groups are called via the *.ndx file (default: index.ndx)
> Be aware that 'pull_dim' determines in which diretions (x,y,z) the
> umbrella potential acts. So use N N Y , if you want that the ion can
> move freely (onsidering the pull) in the xy-plane and Y Y Y if you want
> to also restrit the movement in the xy-plane.
>
>
> Am 12.07.2013 17:32, schrieb gmx-users-request at gromacs.org:
>> Allright.
>> As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system.
>> An ion is considered in center of the each window, the reaction coordinate is set to z,? so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly:
>> ; Pull code
>> pull??????????? = umbrella
>> pull_geometry?? = position
>> pull_dim??????? = N N Y
>> pull_start????? = yes
>> pull_ngroups??? = 1
>> pull_group0???? = COM of protein
>> pull_group1???? = ion
>> pull_init1????? = 0
>> pull_rate1????? = 0.0
>> pull_k1???????? = 4000????? ; kJ mol^-1  nm^-2
>> pull_nstxout??? = 1000????? ; every 2 ps
>> pull_nstfout??? = 1000????? ; every 2 ps
>>
>>
>> IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group?
>>
>> Would you please give me any suggestions?
>>
>> Thanks for all your time and consideration.
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Justin Lemkul<jalemkul at vt.edu>
>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>> Cc:
>> Sent: Friday, July 12, 2013 1:41 AM
>> Subject: Re: [gmx-users] Umbrella Sampling settings
>>
>>
>>
>> On 7/11/13 5:10 PM, Shima Arasteh wrote:
>>>> Thanks for your reply.
>>>>
>>>> But when I don't understand why these extra lines are needed to set when are not advantageous practically!:-(
>>>>
>> There's nothing "extra."? Everything here has a functional purpose.
>>
>> -Justin
>>
>>>>
>>>> Sincerely,
>>>> Shima
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: Justin Lemkul<jalemkul at vt.edu>
>>>> To: Shima Arasteh<shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users<gmx-users at gromacs.org>
>>>> Cc:
>>>> Sent: Friday, July 12, 2013 1:37 AM
>>>> Subject: Re: [gmx-users] Umbrella Sampling settings
>>>>
>>>>
>>>>
>>>> On 7/11/13 4:21 PM, Shima Arasteh wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window.
>>>>>> Some mdp file settings for running US, as I found in US tutorial are :
>>>>>> ; Pull code
>>>>>> pull? ? ? ? ? ? = umbrella
>>>>>> pull_geometry?? = distance
>>>>>> pull_dim? ? ? ? = N N Y
>>>>>> pull_start? ? ? = yes
>>>>>> pull_ngroups? ? = 1
>>>>>> pull_group0? ?? = Chain_B
>>>>>> pull_group1? ?? = Chain_A
>>>>>> pull_init1? ? ? = 0
>>>>>> pull_rate1? ? ? = 0.0
>>>>>> pull_k1? ? ? ?? = 4000? ? ? ; kJ mol^-1  nm^-2
>>>>>> pull_nstxout? ? = 1000? ? ? ; every 2 ps
>>>>>> pull_nstfout? ? = 1000? ? ? ; every 2 ps
>>>>>>
>>>>>>
>>>>>> But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling!
>>>>>>
>>>>
>>>> All of them are related to umbrella sampling.? Pulling (steered MD) and umbrella
>>>> sampling simply use common parts of the "pull code" in Gromacs because US
>>>> requires a restraint potential.? Whether or not that restraint potential induces
>>>> net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate,
>>>> restrain to a given set of conditions) is the only difference.? Both processes
>>>> require reference and "pull" groups, geometry information, etc.
>>>>
>>>> -Justin
>>>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

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