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

[Justin Lemkul]

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.

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
>

-- 
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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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