[gmx-users] Re: gmx-users Digest, Vol 80, Issue 41

Gerrit Groenhof ggroenh at gwdg.de
Mon Dec 6 20:54:54 CET 2010


Without-qmmm-mopac will not lead to compilation of the mopac interface source code. 

What is the compilation error?

Gerrit



> 
>   1. MOPAC gromacs mdreun error (vidhya sankar) (vidhya sankar)
>    
> 
> Message: 1
> Date: Mon, 6 Dec 2010 18:34:00 +0530 (IST)
> From: vidhya sankar <scvsankar_agr at yahoo.com>
> Subject: [gmx-users] MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users at gromacs.org
> Message-ID: <665887.73042.qm at web95501.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Gerrit sir,
>               Thank you for your atonce reply 
> my mopac stand alone binary works well  i have tested using ./run_mopac7 tests/force
> but mdrun is not properly linked aganist libmopac.a 
>  i am using the following command to  configure 
> ./configure --disable-float --without-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac LDFLAGS=-L/usr/local/lib
> if i use --with-qmmm-mopac i end in  make error (compilation  error) 
>  also how to check how to check the link of mdrun aganist libmopac.a  is there is any command for this?
> i am expecting your precious reply thanks in advance
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --- On Mon, 6/12/10, Gerrit Groenhof <ggroenh at gwdg.de> wrote:
> 
> From: Gerrit Groenhof <ggroenh at gwdg.de>
> Subject: Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users at gromacs.org
> Date: Monday, 6 December, 2010, 12:57 PM
> 
> Please check if your stand-alone mopac binary works properly. Also check if the mdrun binary is linked against the libmopac.a
> 
> Gerrit
>> Message: 2
>> Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST)
>> From: vidhya sankar<scvsankar_agr at yahoo.com>
>> Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
>> To: gmx-users at gromacs.org
>> Message-ID:<157886.66733.qm at web95506.mail.in.yahoo.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> Dear Gerrit  sir,
>>                  Thank you for your previous reply i tried as u said with  -nt 1 option in mdrun but still i have got hte following error when i run mdrun_d
>> QM/MM calculation requested.
>> there we go!
>> Layer 0
>> nr of QM atoms 2
>> QMlevel: PM3/STO-3G
>> Program mdrun_d, VERSION 4.5.3
>> Source code file: qmmm.c, line: 697
>> Fatal error:
>> Semi-empirical QM only supported with Mopac.
>>    but i configured gromacs properly with mopac. how to solve the problem
>>    is ther is any link that i have not made available ? i am expecting your worthfull reply thanks isn advance
>> 
>> 
> 
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> ------------------------------
> 
> Message: 2
> Date: Mon, 06 Dec 2010 18:40:36 +0100
> From: Sebastian Fritsch <fritsch at mpip-mainz.mpg.de>
> Subject: Re: [gmx-users] Constraining two virtual sites
> To: gmx-users at gromacs.org
> Message-ID: <4CFD2014.1080802 at mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi again,
> 
> 
> unfortunately I would need the constraint for a large number of molecules, say ~1000 i.e. 2000 vsites representing a few atoms each.
> The constraint length should however be the same for each molecule. 
> 
> Assigning groups for each constraint group would not be possible due to the group limit I guess.
> The do_constraint function in pull.c does not look too complicated, do you think it would be reasonable to adapt it a bit and call it
> from some function like calc_bonds which comes after vsite construct and before vsite spread? The constraint forces in my case should be
> be completely determined by the vsites, or am I wrong? Is there an easier solution?
> 
> 
> Thank you,
> Sebastian
> 
>> Hi,
>> 
>> Unfortunately constraints can not be applied to virtual sites and grompp apparently
>> does not not check for this. I will add a check.
>> Constraints between virtual sites can lead to very complex constraint equations
>> between the masses involved. Thus the general case if difficult to implement.
>> Your cases seems quite simple and could be done with the pull code,
>> if it would support more than one reference group, which I was thinking to implement.
>> 
>> How many molecules do you have?
>> 
>> Berk
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 06 Dec 2010 13:56:04 -0500
> From: nishap.patel at utoronto.ca
> Subject: [gmx-users] Energy-groups?
> To: gmx-users at gromacs.org
> Message-ID: <20101206135604.dgzv1f90bk08ogw4 at webmail.utoronto.ca>
> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
> 	format="flowed"
> 
> Hello,
> 
>    I want to plot the interaction potential energy between my solute  
> and solvent. In my .mdp file I did not mention anything under  
> energygrps,so I am thinking it calculates the energies for the whole  
> system. But is there a way I can extract say for example LJ-14 term  
> between my solute and solvent using the same .edr file? Or would I  
> have to specify my energygrps and run the simulation again.
> 
> Thanks.
> 
> Nisha
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 06 Dec 2010 13:59:23 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Energy-groups?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CFD328B.6040308 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> nishap.patel at utoronto.ca wrote:
>> Hello,
>> 
>>   I want to plot the interaction potential energy between my solute and 
>> solvent. In my .mdp file I did not mention anything under energygrps,so 
>> I am thinking it calculates the energies for the whole system. But is 
>> there a way I can extract say for example LJ-14 term between my solute 
>> and solvent using the same .edr file? Or would I have to specify my 
>> energygrps and run the simulation again.
>> 
> 
> 1-4 interactions are intramolecular, so there should be no solute-solvent 1-4 
> term.  If you want nonbonded potentials decomposed, yes, you have to rerun your 
> trajectory (mdrun -rerun, not from scratch) with a .tpr file specifying the 
> desired groups.
> 
> -Justin
> 
>> Thanks.
>> 
>> Nisha
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 06 Dec 2010 14:31:38 -0500
> From: nishap.patel at utoronto.ca
> Subject: Re: [gmx-users] Energy-groups?
> To: gmx-users at gromacs.org
> Message-ID: <20101206143138.irw4yddc6c4gkscs at webmail.utoronto.ca>
> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
> 	format="flowed"
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
> Thanks Justin! I do want the non-bonded potential between my solute  
> and solvent. So in my .mdp file I put my solute and solvent as  
> energygrps and ran mdrun using this command:
>   mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)
> 
> Is that correct? I don't understand how it would be faster or any  
> different from running the simulation from scratch, because in my .mdp  
> file it still has time of 100ns. I just modified the energygrps.
> 
> 
>> 
>> 
>> nishap.patel at utoronto.ca wrote:
>>> Hello,
>>> 
>>>  I want to plot the interaction potential energy between my solute  
>>> and solvent. In my .mdp file I did not mention anything under   
>>> energygrps,so I am thinking it calculates the energies for the   
>>> whole system. But is there a way I can extract say for example   
>>> LJ-14 term between my solute and solvent using the same .edr file?   
>>> Or would I have to specify my energygrps and run the simulation   
>>> again.
>>> 
>> 
>> 1-4 interactions are intramolecular, so there should be no
>> solute-solvent 1-4 term.  If you want nonbonded potentials decomposed,
>> yes, you have to rerun your trajectory (mdrun -rerun, not from scratch)
>> with a .tpr file specifying the desired groups.
>> 
>> -Justin
>> 
>>> Thanks.
>>> 
>>> Nisha
>>> 
>> 
>> -- 
>> ========================================
>> 
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> ========================================
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Mon, 06 Dec 2010 14:52:05 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Energy-groups?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CFD3EE5.6020001 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> nishap.patel at utoronto.ca wrote:
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> 
>> Thanks Justin! I do want the non-bonded potential between my solute and 
>> solvent. So in my .mdp file I put my solute and solvent as energygrps 
>> and ran mdrun using this command:
>>  mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)
>> 
>> Is that correct? I don't understand how it would be faster or any 
>> different from running the simulation from scratch, because in my .mdp 
>> file it still has time of 100ns. I just modified the energygrps.
>> 
> 
> It should be significantly faster.  In this case, mdrun is not doing the 
> integration, it's simply using the known positions to re-calculate energies.
> 
> -Justin
> 
>> 
>>> 
>>> 
>>> nishap.patel at utoronto.ca wrote:
>>>> Hello,
>>>> 
>>>>  I want to plot the interaction potential energy between my solute 
>>>> and solvent. In my .mdp file I did not mention anything under  
>>>> energygrps,so I am thinking it calculates the energies for the  whole 
>>>> system. But is there a way I can extract say for example  LJ-14 term 
>>>> between my solute and solvent using the same .edr file?  Or would I 
>>>> have to specify my energygrps and run the simulation  again.
>>>> 
>>> 
>>> 1-4 interactions are intramolecular, so there should be no
>>> solute-solvent 1-4 term.  If you want nonbonded potentials decomposed,
>>> yes, you have to rerun your trajectory (mdrun -rerun, not from scratch)
>>> with a .tpr file specifying the desired groups.
>>> 
>>> -Justin
>>> 
>>>> Thanks.
>>>> 
>>>> Nisha
>>>> 
>>> 
>>> -- 
>>> ========================================
>>> 
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> 
>>> ========================================
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> 
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> ------------------------------
> 
> -- 
> gmx-users mailing list
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> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> 
> End of gmx-users Digest, Vol 80, Issue 41
> *****************************************

--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/




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