for PCA i used the g_covar followed by g_anaeig.
i used the command line for g_covr as
g_covar -f full.xtc -s full.tpr -o eig.xvg
I have selected the protein for least square fit and main chain for
covarience analysis.
There is a warning message.
WARNING: number of atoms in tpx (312) and trajectory (1061) do not match

The abve comman gave the files average.pdb, eigenvec.trr and eig.xvg
Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
The commnan line for g_anaeig is given below.
g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
For least square fit i have selected the protein and same for the
eigenvectors
This gave the following message;
There were 40 inconsistent shifts. Check your topology
where is the problem occured?

On Wed, Mar 11, 2015 at 3:31 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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> Today's Topics:
>
>    1. Binding free energy of an ion from alchemical     transformation
>       (Wojciech Kope?)
>    2. umbrella sampling tutorial (Ming Tang)
>    3. Re: enemat output (Mark Abraham)
>    4. g_anaeig error (tasneem kausar)
>    5. Thermostats and MSD (sujithkakkat .)
>    6. Re: g_anaeig error (Tsjerk Wassenaar)
>    7. Compiler (Alexander Tzanov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Mar 2015 09:23:53 +0100
> From: Wojciech Kope? <9000...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Binding free energy of an ion from alchemical
>         transformation
> Message-ID:
>         <
> cak_bonfb_m2mgxumw8gswhfzbtdifp4lkjw4pgbhvy3p5uc...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I'm thinking about performing free energy calculations for a protein that
> binds cations,  using alchemical transformation method. In the simplest
> case I'd transform an ion (one atom) into a naked particle; however in this
> case I'd get a non-zero overall charge of the system during the charge
> decoupling. I'm aware of some corrections for that and also that Gromacs
> probably neutralises the charge with PME (?). Another approach I've been
> thinking of is to simultaneously couple a naked particle somewhere in the
> bulk with the environment, switching on the charge in a same way as the
> charge of the ion is being switched off. In this way, the charge would be 0
> all the time, and at the end of the simulation would yield the protein with
> an empty binding site and the ion somewhere in the bulk. Are there any
> obvious pitfalls with this approach?
>
> Thank you,
> Wojciech
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Mar 2015 08:17:42 +0000
> From: Ming Tang <m21.t...@qut.edu.au>
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>         <gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: [gmx-users] umbrella sampling tutorial
> Message-ID:
>         <
> dm2pr0101mb10690504f9ed567db577b697b6...@dm2pr0101mb1069.prod.exchangelabs.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I was learning the Umbrella Sampling tutorial step by step on Gromacs
> 5.0.4.
> Everything was fine until I got to the step five (run the continuous
> pulling simulation).
> Then I turned to the 5.0.4 manual, and tried to modify the pull code, but
> failed.
>
> ; Pull code in tutorial
> pull            = umbrella
> pull_geometry   = distance      ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A
> pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000          ; kJ mol^-1 nm^-2
>
> ; COM pulling I modified
> pull            = umbrella
> pull_geometry        = distance  ; simple distance increase
> pull_dim             = N N Y
> pull_start           = yes       ; define initial COM distance > 0
> pull_coord1-groups   = 2
> pull-group1-name     = Chain_B
> pull_group2-name     = Chain_A
> pull-coord1-rate     = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k        = 1000      ; kJ mol^-1 nm^-2
>
> Fatal error:
> Group Chain_B referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
>
> Index:
> [ r_1-27 ]
>    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
>  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
>  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
>  136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
>  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
>  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
>  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
>  196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
>  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
>  226
> [ r_28-54 ]
> 227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
>  242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
>  257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
>  272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
>  287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
>  302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
>  317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
>  332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
>  347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
>  362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
>  377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
>  392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
>  407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
>  422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
>  437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
>  452
>
> Could anybody tell me what's wrong with the COM pulling code I modified?
>
> Thanks in advance!
>
> Regards,
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 11 Mar 2015 09:35:57 +0100
> From: Mark Abraham <mark.j.abra...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Subject: Re: [gmx-users] enemat output
> Message-ID:
>         <
> camnumatrubz5arfdzcb-bz+1zrbdoqff68ahgw-iemicm7y...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On 11/03/2015 3:44 am, "Diogo Martins de S?" <sadi...@mol.bio.br> wrote:
> >
> > Hi guys,
> >
> > Can any one show a picture of how a normal enemat output should look
> > like?
> >
> > Since the bug in enemat was only fixed in version 4.6.5, I have a very
> > basic question:
> >
> > Can I install a newer version of gromac (say 5) and use its enemat to
> > treat .edr files from older versions (i.e. 4.5.3 and 4.6.3)??
>
> Yes
>
> Mark
>
> > Many thanks
> >
> > Diogo
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Mar 2015 15:01:29 +0530
> From: tasneem kausar <tasneemkausa...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] g_anaeig error
> Message-ID:
>         <CAFaK4UZND1MO2bzEhAJJp9upAJJXDxk-V1UjcLU6W8m=-
> re...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> for PCA i used the g_covar followed by g_anaeig.
> for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
> these files are generated by g_covar.
> g_anaeig gives the following message;
> There were 40 inconsistent shifts. Check your topology
> where is the problem occured?
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 11 Mar 2015 15:12:09 +0530
> From: "sujithkakkat ." <sujithk...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Thermostats and MSD
> Message-ID:
>         <CAKaGHgtCBQNJU2_YLPKX=dAimKJMVy=
> s36carsstjbksuad...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>
>   I am simulating a system of small hydrophobic solutes ( CH4)  dissolved
> in water. Simulations are performed in the NPT simulation, and I would like
> to determine the diffusion coefficients from MSD plots. I have two related
> questions;
>
> (1)  Is the thermostat going to seriously affect the diffusivity of the
> molecules. I am using Nose-Hoover thermostat with a time constant of 0.2
> ps. Is the choice of time constant very crucial while studying diffusivity.
> Should I avoid thermostat and go for NVE simulations for studying
> diffusivity.
>
> (2) From radial distribution functions, it is found that there is
> association between the hydrophobic solvents. I would like to know, if in
> case a small cluster of the hydrophobic solutes are formed, then the
> whether the rotational motion of these clusters contribute to dispalcement
> in the MSD calculation.
>
> Please comment.
>
> Regards,
> Sujith.
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 11 Mar 2015 10:51:13 +0100
> From: Tsjerk Wassenaar <tsje...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Subject: Re: [gmx-users] g_anaeig error
> Message-ID:
>         <
> cabze1sgyvzadcjsklrso84rwtfnjrm6ubjgk6txp34jn8kr...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Tasneem,
>
> Please provide a complete workflow, with commands and selections.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Mar 11, 2015 at 10:31 AM, tasneem kausar <
> tasneemkausa...@gmail.com>
> wrote:
>
> > for PCA i used the g_covar followed by g_anaeig.
> > for g_anaeig i am using the eigenvec.trr file and averagr.pdb file
> > these files are generated by g_covar.
> > g_anaeig gives the following message;
> > There were 40 inconsistent shifts. Check your topology
> > where is the problem occured?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 11 Mar 2015 09:49:50 +0000
> From: Alexander Tzanov <alexander.tza...@csi.cuny.edu>
> To: gmx-users <gromacs.org_gmx-users@maillist.sys.kth.se>
> Cc: "alex.tza...@csi.cuny.edu" <alex.tza...@csi.cuny.edu>
> Subject: [gmx-users] Compiler
> Message-ID:
>         <f5699b2497cefd418883db2ed5cfcb36e83ce...@mbox1.flas.csi.cuny.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all I am trying to install the 5.0.4 with GPU support with Intel 15
> compiler and 1.8.4 openmpi.I got errors that  only Intel 14 is supported.
> Is this true? And if so do you plan to have tested/port GMX with latest
> Intel compiler?
>
> Thanks Alex
>
> ________________________________
> Connect with CSI on Social Media><http://csitoday.com/social_media/>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 131, Issue 49
> ******************************************************
>
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