g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it takes the default index file, so there isnt any wrong in selecting the atoms.
On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham <[email protected]>wrote: > On 13/09/2011 4:14 PM, aiswarya pawar wrote: > > Mark, > > the command line goes like this- > > g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 > > > This command line is not using an index file. The index groups defined for > the grompp that produced the .tpr are being used (which may be the default > ones, depending what you did). Please copy and show the interactive input > you made to g_dist after it showed the groups it knew about. > > > > the index file has group1- a_1322 ( this is just a single atom from a > protein. its in sidechain) > group2- a_OW ( this is water atoms) > > > Your output is listing the time of the frame, and the residue number, > residue name, atom number, and atom name of the matching atom. Apparently a > water molecule can sometimes be closer than 0.2nm, and sometimes not. > > Mark > > > > now as per the utility it should give me and output as- > > t:1 1322 a 54119 OW 0.389 > > but am getting something different > > On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham <[email protected]>wrote: > >> On 13/09/2011 3:40 PM, aiswarya pawar wrote: >> >> >> Hi Mark, >> >> The -dist option says- print all the atoms in group 2 that are closer than >> a certain distance to the center of mass of group 1. >> That means it should give me the distance from OW to protein atom. >> >> >> If you choose correct groups that are correctly defined with respect to >> your trajectory and use a large enough distance cutoff. >> >> >> >> And when am already specifying only one atom from protein ie say 1322. why >> do i get this kind of output- >> >> >> We can't tell. We don't know what your command line is, what's in your >> simulation system, the contents of your index groups, or which groups you've >> selected for which role. Clearly something is not working properly, and our >> time constraints mean that we're going to assume you've done something >> wrong, in the absence of evidence to the contrary. >> >> Mark >> >> >> >> t: 275 20230 SOL 62618 OW 0.341434 (nm) >> t: 275 22019 SOL 67985 OW 0.171584 (nm) >> t: 276 10768 SOL 34232 OW 0.303328 (nm) >> t: 276 20230 SOL 62618 OW 0.325176 (nm) >> t: 276 22019 SOL 67985 OW 0.187259 (nm) >> t: 277 10768 SOL 34232 OW 0.306008 (nm) >> t: 277 20230 SOL 62618 OW 0.326195 (nm) >> t: 277 22019 SOL 67985 OW 0.181089 (nm) >> t: 278 10768 SOL 34232 OW 0.274507 (nm) >> t: 278 22019 SOL 67985 OW 0.292652 (nm) >> t: 279 10618 SOL 33782 OW 0.319922 (nm) >> t: 280 10618 SOL 33782 OW 0.330082 (nm) >> t: 280 22019 SOL 67985 OW 0.330203 (nm) >> t: 281 8273 SOL 26747 OW 0.278731 (nm) >> t: 281 10618 SOL 33782 OW 0.325434 (nm) >> t: 281 11535 SOL 36533 OW 0.200327 (nm) >> t: 281 17036 SOL 53036 OW 0.343946 (nm) >> t: 282 8273 SOL 26747 OW 0.256558 (nm) >> t: 282 11535 SOL 36533 OW 0.327147 (nm) >> t: 283 8273 SOL 26747 OW 0.165061 (nm) >> t: 283 10618 SOL 33782 OW 0.306578 (nm) >> t: 283 17191 SOL 53501 OW 0.333075 (nm) >> t: 284 8273 SOL 26747 OW 0.19427 (nm) >> t: 284 10618 SOL 33782 OW 0.321927 (nm) >> t: 284 17191 SOL 53501 OW 0.30832 (nm) >> >> >> >> >> On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham >> <[email protected]>wrote: >> >>> On 13/09/2011 2:27 PM, [email protected] wrote: >>> >>> Iam -dist option because I need the distance between two groups >>> >>> >>> That is not what g_dist -dist does. Please read g_dist -h. >>> >>> >>> excluding -dist gives me X,Y,Z output which I don't want. >>> >>> >>> And other output which you do, but you have to use -o to get it. Read >>> g_dist -h. >>> >>> >>> And am not specifying an -o. >>> >>> >>> You need to specify -o to achieve your purpose. However, as I said quite >>> a while ago, there is no value in measuring the distance between a protein >>> phase and a water phase if they are in contact... >>> >>> Mark >>> >>> >>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for >>> it! >>> >>> -----Original Message----- >>> From: "Justin A. Lemkul" <[email protected]> <[email protected]> >>> Date: Mon, 12 Sep 2011 22:35:28 >>> To: <[email protected]> <[email protected]>; Discussion list >>> for GROMACS users<[email protected]> <[email protected]> >>> Reply-To: [email protected] >>> Subject: Re: [gmx-users] g_dist error >>> >>> >>> [email protected] wrote: >>> >>> Even if I specify an atom say 1277 atom number to find distance against >>> the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause >>> even after specifying one atom from a protein why doesn't it give me the >>> result for the SOL. >>> >>> >>> >>> As was suggested several messages ago, please do NOT combine -o and -dist. >>> If >>> you want to measure a distance, use -o. If you want g_dist to print a list >>> of >>> atoms that satisfy some given criteria, use -dist, but not together. >>> >>> -Justin >>> >>> >>> Thanks >>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for >>> it! >>> >>> -----Original Message----- >>> From: "Justin A. Lemkul" <[email protected]> <[email protected]> >>> Sender: [email protected] >>> Date: Mon, 12 Sep 2011 07:52:54 >>> To: Discussion list for GROMACS users<[email protected]> >>> <[email protected]> >>> Reply-To: [email protected], >>> Discussion list for GROMACS users <[email protected]> >>> <[email protected]> >>> Subject: Re: [gmx-users] g_dist error >>> >>> >>> >>> aiswarya pawar wrote: >>> >>> hi Justin, >>> >>> As far i referred the OW,HW1 etc are water atoms so how can it be >>> distance between the SOL protein atoms, instead it is SOL water atoms. >>> >>> >>> The printed distance indicates that there is a certain water molecule that >>> is >>> just over 2 hydrogen bonding lengths away from your protein's backbone. >>> Sounds >>> normal to me. >>> >>> -Justin >>> >>> >>> Thanks >>> >>> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <[email protected] >>> <mailto:[email protected]> <[email protected]>> wrote: >>> >>> >>> >>> aiswarya pawar wrote: >>> >>> Hi Users, >>> >>> Am using g_dist to find the distance between water and protein. >>> but my output has the values of SOL-water distance. >>> >>> t: 1 136 SOL 2336 OW 0.772373 (nm) >>> >>> >>> This is not a water-water distance, it is the output of the -dist >>> option telling you that water molecule 136 has its OW atom at >>> 0.7723273 nm from whatever your reference group is. >>> >>> -Justin >>> >>> -- >>> ==============================__========== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080 >>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin >>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >>> ==============================__========== >>> -- >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> <[email protected]> >>> http://lists.gromacs.org/__mailman/listinfo/gmx-users >>> <http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> <http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at >>> http://www.gromacs.org/__Support/Mailing_Lists/Search >>> <http://www.gromacs.org/Support/Mailing_Lists/Search> >>> <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 [email protected] >>> <mailto:[email protected]> <[email protected]>. >>> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists >>> <http://www.gromacs.org/Support/Mailing_Lists> >>> <http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> >>> >>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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