Fwd: Fw: Fwd: [gmx-users] position restraints

[Mark Abraham]

On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/18/13 3:42 AM, Shima Arasteh wrote:
>
>> Thanks for all your replies.
>> But I' d like to know what the meanings of S and D are? Why sometimes we
>> should write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
>>
>>
> I already explained what the "D" prefix means.  If this is unclear to you,
> please read about cpp macros.  When processing a topology, grompp works
> just like cpp works on C source code.
>

See also http://www.gromacs.org/Documentation/Include_File_Mechanism

Mark

The choice between POSRE and POSRES is completely irrelevant except for
> your own usage and consistency in so doing.  Gromacs defaults to using
> POSRES to indicate POSition REStraints.  If you build some custom topology,
> you can use whatever you want.  it doesn't matter at all, as long as you
> are consistent in invoking it.
>
> -Justin
>
>
>
>>
>> Sincerely,
>> Shima
>>
>>
>> ______________________________**__
>> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>> To: Justin Lemkul <jalemkul at vt.edu>; Discussion list for GROMACS users <
>> gmx-users at gromacs.org>
>> Sent: Monday, March 18, 2013 10:35 AM
>> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
>>
>> To solve the problem, I changed all DPOSREs in if statments to POSRE.
>> Again I get the fatal error. This error states that I have inserted
>> topology section "position_restraints" in a wrong place. I checked again
>> the itp files included in my top file. They are matched correctly!  Did I
>> modified the settings incorrectly?
>>
>> What would be other potent problems?
>>
>> Please help me.
>> Thanks for your help.
>>
>>
>>
>> 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: Sunday, March 17, 2013 5:19 PM
>> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
>>
>>
>>
>> On 3/17/13 6:50 AM, Shima Arasteh wrote:
>>
>>> Thanks for your replies.
>>> As you suggested, I did as follows:
>>> 1. made index groups of two chains of my protein
>>> 2.Then applied genrestr in this command to generate 2 itp files:
>>> chainA_posre.itp and chainB_posre.itp
>>> #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 100000 100000
>>> 100000 -n index-chain.ndx
>>> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 100000 100000
>>> 100000 -n index-chain.ndx
>>>
>>> 3.Next, I included the itp files as follow in my top file:
>>>
>>> ; Include chain topologies
>>> #include "topol_Protein_chain_A.itp"
>>> #ifdef DPOSRE
>>> #include "chainA_posre.itp"
>>> #endif
>>> #include "topol_Protein_chain_B.itp"
>>> #ifdef DPOSRE
>>> #include "chainB_posre.itp"
>>> #endif
>>>
>>> 4. I also added this line to my mdp file:
>>> define         = -DPOSRE
>>>
>>> 5. In addition I added these at the top of itp files for bothe
>>> restrained chains:
>>> #ifdef DPOSRE
>>> #endif
>>>
>>> Now when I run the command :
>>> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr
>>>
>>> I don't get any errors.
>>> But when I run the mdrun I don't see any position restraint terms in my
>>> log file.
>>> Would you please let me know your suggestions in this about? Did I do
>>> any steps by mistake?
>>>
>>>
>> Yes, again there is a problem with the #ifdef statements.  If you use:
>>
>> #ifdef DPOSRE
>> ...
>> #endif
>>
>> the corresponding "define" statement is -DDPOSRE.  Think of the first "D"
>> in the
>> "define" statement as "I am defining the following string to be true."
>>  Your
>> .mdp file corresponds to the use of:
>>
>> #ifdef POSRE
>> ...
>> #endif
>>
>> -Justin
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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