using new parameters for Mg2+

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Hi, I'm working on a QMMM calculation and would like to change some vdw parameters of Mg2+ (included in QM part) from the original amber parameters provided. So what I need to do is create an amber.par file in the nwchem format, change original parameters to the new ones, AND then place this file to the directory I would like to run prepare directive task, right? So the new parameters will be used instead of the old ones??

Any comments are very welcome.

Best,
Tee
Edited On 3:22:13 PM PDT - Wed, Jul 24th 2013 by Tpirojsi

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In according to my knowledge, yes. If there are different parameters for the same kind of atom, the order is given by the .nwchemrc file and the last one is the folder in which you are running the job.

I never tried, but I think you can prepare an amber.par file with only the data that you want to change and the others will be taken from the other amber.par file.

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Quote:Varnon Aug 29th 9:37 am
In according to my knowledge, yes. If there are different parameters for the same kind of atom, the order is given by the .nwchemrc file and the last one is the folder in which you are running the job.

I never tried, but I think you can prepare an amber.par file with only the data that you want to change and the others will be taken from the other amber.par file.


Thank you Varnon. I have one more question. Are the 'Q' flags necessary in the amber.par file for any QM atoms with modified parameters. I have seen in the following page http://www.nwchem-sw.org/index.php/QMMM_Appendix#Generation_of_new_fragment_files that the newly created atom types are flagged with Q. My case is just modifying parameters though. And when the topology file was created I did see the atom types defined as QM atoms with the prepare module were all 'Q' flagged. So just wondering when 'Q' flags are needed to be considered.

Best,
Tee

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Quote:Tpirojsi Oct 18th 3:27 am
Quote:Varnon Aug 29th 9:37 am
In according to my knowledge, yes. If there are different parameters for the same kind of atom, the order is given by the .nwchemrc file and the last one is the folder in which you are running the job.

I never tried, but I think you can prepare an amber.par file with only the data that you want to change and the others will be taken from the other amber.par file.


Thank you Varnon. I have one more question. Are the 'Q' flags necessary in the amber.par file for any QM atoms with modified parameters. I have seen in the following page http://www.nwchem-sw.org/index.php/QMMM_Appendix#Generation_of_new_fragment_files that the newly created atom types are flagged with Q. My case is just modifying parameters though. And when the topology file was created I did see the atom types defined as QM atoms with the prepare module were all 'Q' flagged. So just wondering when 'Q' flags are needed to be considered.

Best,
Tee


Also I'm wondering how to check whether the new parameters overwrite the old ones. I've tried 2 cases, first with the old Mg2+ parameter and the second with a new Mg2+ parameter (put inthe directory I run prepare module). However, when I used 'diff' command to compare between topology files of these two cases, I got no differences except for the date of file creation. I have also tried to search for vdw parameters in topology file to match with the values in amber.par file but couldn't find any.

I'm aware that amber.par used in nwchem is format sensitive so I carefully checked and had everything to be the same as the original amber.par files.

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Quote:Tpirojsi Oct 18th 5:47 pm
Quote:Tpirojsi Oct 18th 3:27 am
Quote:Varnon Aug 29th 9:37 am
In according to my knowledge, yes. If there are different parameters for the same kind of atom, the order is given by the .nwchemrc file and the last one is the folder in which you are running the job.

I never tried, but I think you can prepare an amber.par file with only the data that you want to change and the others will be taken from the other amber.par file.


Thank you Varnon. I have one more question. Are the 'Q' flags necessary in the amber.par file for any QM atoms with modified parameters. I have seen in the following page http://www.nwchem-sw.org/index.php/QMMM_Appendix#Generation_of_new_fragment_files that the newly created atom types are flagged with Q. My case is just modifying parameters though. And when the topology file was created I did see the atom types defined as QM atoms with the prepare module were all 'Q' flagged. So just wondering when 'Q' flags are needed to be considered.

Best,
Tee


Also I'm wondering how to check whether the new parameters overwrite the old ones. I've tried 2 cases, first with the old Mg2+ parameter and the second with a new Mg2+ parameter (put inthe directory I run prepare module). However, when I used 'diff' command to compare between topology files of these two cases, I got no differences except for the date of file creation. I have also tried to search for vdw parameters in topology file to match with the values in amber.par file but couldn't find any.

I'm aware that amber.par used in nwchem is format sensitive so I carefully checked and had everything to be the same as the original amber.par files.


Never mind. I think I knew where my mistake was.
Edited On 12:44:16 PM PDT - Fri, Oct 18th 2013 by Tpirojsi


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