[gmx-users] virtual sites

[Neha Gandhi]

Dear Users,

I have a system consisting of peptides and a linear carbohydrate.
Initially I tried to simulate these peptides using virtual sites and
it worked. I can use pdb2gmx for building virtual sites on protein
whereas I have an itp file for the carbohydrate. Is it possible to
apply virtual site to a carbohydrate along with the peptides?

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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Re: [gmx-users] lmc-stats

[Michael Shirts]

Hi, Andrew-

The choice of lmc-stats only affects the calculation of the weights,
it does not affect the calculation of the transition matrix.

There are two possibilities for the transition matrix; the estimated
one (which is just called 'Transition Matrix' -- we should probably
have a better name), and the empirical one.  The empirical transition
matrix is just transition counts. The first one is an ensemble average
of P(k|x); for neighbor moves, this is just the average of the barker
transition probabilities (plus the choice of going up or down),

Let me know if this is useful.  Not that many people have used this
code, thus there are likely ways that it can be improved for better
utility.  I generally haven't tried to calculate free energy
differences from the transition matrix, though it should give
consistent results with the other methods.

Best,

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shi...@virginia.edu
(434)-243-1821

On Mon, Oct 28, 2013 at 11:13 PM, Andrew S. Paluch  wrote:
> When performing free energy calculations using the expanded ensemble method,
> there is a barker and metropolis option for lmc-stats. Are the corresponding
> transition probabilities computed with or without the weighting factors?
> That is, are these probabilities biased or not?
>
> Thank you,
>
> Andrew
>
> --
>
> Andrew S. Paluch, PhD
> Department of Chemical, Paper, and Biomedical Engineering
> Miami University
> paluc...@miamioh.edu
> (513) 529-0784
> --
> gmx-users mailing listgmx-users@gromacs.org
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> * Please search the archive at
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[gmx-users] lmc-stats

[Andrew S. Paluch]

When performing free energy calculations using the expanded ensemble 
method, there is a barker and metropolis option for lmc-stats. Are the 
corresponding transition probabilities computed with or without the 
weighting factors? That is, are these probabilities biased or not?


Thank you,

Andrew

--

Andrew S. Paluch, PhD
Department of Chemical, Paper, and Biomedical Engineering
Miami University
paluc...@miamioh.edu
(513) 529-0784
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Re: [gmx-users] mdrun cpt

[Pavan Ghatty]

Now /afterok/ might not work since technically the job is killed due to
walltime limits - making it not ok. So I suppose /afterany/ is a better
option. But I do appreciate your warning about spamming the queue and yes I
will re-read PBS docs.


On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham wrote:

> On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty  >wrote:
>
> > Mark,
> >
> > The problem with one .tpr file set for 100ns is that when job number
> (say)
> > 4 hits the wall limit, it crashes and never gets a chance to submit the
> > next job. So it's not really automated.
> >
>
> That's why I suggested -maxh, so you can have an orderly shutdown. (Though
> if a job can get suspended, that won't always help, because mdrun can't
> find out about the suspension...)
>
> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
> > till job 4 ends.
>
>
> Sure - read your PBS docs and find the environment variable to read so that
> job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on
> it. But don't tell your sysadmins where I live. ;-) Seriously, if you live
> on this edge, you could spam infinite jobs, which tends to get your account
> cut off. That's why you want the afterok hold - you only want the next job
> to start if the exit code from the first script correctly indicates that
> mdrun exited correctly. Test carefully!
>
> Mark
>
> But the PBS queuing system is sometime weird and takes a
> > bit of time to recognize a job and give back its jobID. So I could submit
> > job 5 but be unable to change its status to /hold/ because PBS does not
> > return its ID. Another problem is that if resources are available, job 5
> > could start before I ever get a chance to /hold/ it.
> >
> >
> >
> >
> > On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham  > >wrote:
> >
> > > On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty  > > >wrote:
> > >
> > > > I have need to collect 100ns but I can collect only ~1ns (1000steps)
> > per
> > > > run. Since I dont have .trr files, I rely on .cpt files for restarts.
> > For
> > > > example,
> > > >
> > > > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> > > >
> > > > This runs into a problem when the run gets killed due to walltime
> > > limits. I
> > > > now have a .xtc file which has run (say) 700 steps and a .cpt file
> > which
> > > > was last written at 600th step.
> > > >
> > >
> > > You seem to have no need to use grompp, because you don't need to use a
> > > workflow that generates multiple .tpr files. Do the equivalent of what
> > the
> > > restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
> > .tpr
> > > for the whole 100ns run, and then keep doing
> > >
> > > mdrun -s whole-run -cpi whateverwaslast -deffnm
> whateversuitsyouthistime
> > >
> > > with or without -append, perhaps with -maxh, keeping whatever manual
> > > backups you feel necessary. Then perhaps concatenate your final
> > trajectory
> > > files, according to your earlier choices.
> > >
> > > - To set up the next run I use the .cpt file from 600th step.
> > > > - Now during analysis if I want to center the protein and such,
> > /trjconv/
> > > > needs an .xtc and .tpr file but not a .cpt file. So how does
> /trjconv/
> > > know
> > > > to stop at 600th step?
> > >
> > >
> > > trjconv just operates on the contents of the trajectory file, as
> modified
> > > by things like -b -e and -dt. The .tpr just gives it context, such as
> > atom
> > > names. You could give it a .tpr from any point during the run.
> > >
> > > Mark
> > >
> > > If this has to be put in manually, it becomes
> > > > cumbersome.
> > > >
> > > > Thoughts?
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul 
> > wrote:
> > > >
> > > > >
> > > > >
> > > > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> > > > >
> > > > >> Hello All,
> > > > >>
> > > > >> Is there a way to make mdrun put out .cpt file with the same
> > frequency
> > > > as
> > > > >> a
> > > > >> .xtc or .trr file. From here
> > > > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> > > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see
> that
> > > we
> > > > >> can choose how often (time in mins) the .cpt file is written. But
> > > > clearly
> > > > >> if the frequency of output of .cpt (frequency in mins) and .xtc
> > > > (frequency
> > > > >> in simulation steps) do not match, it can create problems during
> > > > analysis;
> > > > >> especially in the event of frequent crashes. Also, I am not
> storing
> > > .trr
> > > > >> file since I dont need that precision.
> > > > >> I am using Gromacs 4.6.1.
> > > > >>
> > > > >>
> > > > > What problems are you experiencing?  There is no need for .cpt
> > > frequency
> > > > > to be the same as .xtc frequency, because any duplicate frames
> should
> > > be
> > > > > handled elegantly when appending.
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==**=

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Justin Lemkul]

On 10/28/13 8:07 PM, Hari Pandey wrote:

Many thanks to Dr.Lemkul

Yes  mass is 444 in my .top file and I did  "-density 1000 "  because then it
will show the density also.



If you have one molecule in a box of a known size, you don't need any 
command-line flags - you have a mass and a known volume.  Using -density 1000 is 
probably harmless, since it is the default, but you can remove that level of 
complexity in the command (because, again, you are doing things that conflict).



I am wandering how do I find that which  atom name mismatched. The
forcefield folder is in my working directory and there are all files.
atomtypes.atp is there and which contains the atom names  which I posted last 
email


Hard to say.  Your input snippets are incomplete.  A rough calculation of the 
.rtp file gives me a mass of only 375 amu, so I don't know where 444 is coming 
from and it's impossible to tell if you haven't shown us everything or if there 
are mistakes somewhere else.


-Justin


Thanks for your regard
Hari


On Monday, October 28, 2013 4:50 PM, Justin Lemkul  wrote:


On 10/28/13 7:41 PM, Hari Pandey wrote:
 >
 >
 >
 >
 > Thank you so much  Mark.
 >
 > I still did not understand. More detaily.  Atomtypes are only following:
 >
 > atomtypes.atp::
 >
 > H  1.00800 ;  polar H
 > DUM0.0 ;  dummy atom
 > HAL1  1.008000 ;  alphatic proton
 > HAL2  1.008000 ;  alphatic proton
 > HAL3  1.008000 ;  alphatic proton
 > CTL1  12.011000 ;carbonyl C (acetic acid/methyl acetate);;;
 > CTL1  12.011000 ;sp3 carbon with 1 H (-CH1-)
 > CTL2  12.011000 ;carbon of methylene group (-CH2-)
 > CTL3  12.011000 ;carbon of methyl group (-CH3)
 > OBL15.999400 ;acetic acid carboxyl oxygen (e. to protein OB)
 > OCL15.999400 ;acetate oxygen
 > OSL15.999400 ;ester oxygen
 > O2L  15.999400 ;Nucleic acid =O in phosphate or sulfate
 > SL  32.06 ;Sulfate sulfur
 > NA  22.989770; FOR  sodium ion
 >
 >
 > MR.rtp:
 >
 > SSL  1.3600  0
 >  OS1O2L-0.60000
 >  OS2O2L-0.60000
 >  OS3O2L-0.60000
 >  C1  CTL1-0.19000
 >  H1  HAL10.0900  0
 >  C2 CTL2-0.18001
 >  H2  HAL20.0900  1
 >  H3  HAL20.0900  1
 >  C3  CL  0.6300  2 ;
 >  O1  OBL-0.52002
 >  O2  OSL-0.34002
 >  C4  CTL2-0.18003
 > H4  HAL20.0900  3
 >  H5  HAL20.0900  3
 >  C5  CTL1-0.09004
 >  H6  HAL10.0900  4
 >  C6  CTL2-0.18005
 >  H7  HAL20.0900  5
 >  H8  HAL20.0900  5
 > C7  CTL2-0.18006
 >  H9  HAL20.0900  6
 >  H10HAL20.0900  6
 >  C8  CTL2-0.18007
 >  H11HAL20.0900  7
 >  H12HAL20.0900  7
 >  C9  CTL3-0.27008
 >  H13 HAL30.0900  8
 >  H14HAL30.0900  8
 >  H15HAL30.0900  8
 >  C10CTL2-0.18009
 >  H16HAL20.0900  9
 >  H17HAL20.0900  9
 >  C11CTL3-0.270010
 >  H18HAL30.0900   10
 >  H19HAL30.0900  10
 >  H20HAL30.0900  10
 >  C12CL  0.6300  11 ;
 >  O3  OBL-0.520011
 >  O4  OSL-0.340011
 >  C13CTL2-0.180012
 >  H21HAL20.0900   12
 >  H22HAL20.0900  12
 >  C14CTL1-0.090013
 >  H23HAL10.0900  13
 >  C15CTL2-0.180014
 >  H24HAL20.0900  14
 >  H25HAL20.0900  14
 >  C16CTL2-0.180015
 > H26HAL20.0900  15
 >  H27HAL20.0900  15
 >  C17CTL2-0.180016
 >
 >
 > I have A.pdb and  I got A.gro  using this force field.
 >
 >
 > Some part of  A.pdb::
 >
 > REMARK  Created:  Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007
 > CRYST18.760  8.760  8.760  90.00  90.00  90.00 P11
 > MODEL1
 > ATOM  1 S  AOT  151  6.864  -6.902  0.078  1.00  0.00
 > ATOM  2  OS1 AOT  151  7.820  -5.791  -0.815  1.00  0.00
 > ATOM  3  OS2 AOT  151  5.369  -7.134  -0.714  1.00  0.00
 > ATOM  4  OS3 AOT  151  6.589  -6.277  1.657  1.00  0.00
 > ATOM  5  C1  AOT  151  7.728  -8.482  0.

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Hari Pandey]

Many thanks to Dr.Lemkul

Yes  mass is 444 in my .top file and I did  "-density 1000 "  because then it 
will show the density also.

   I am wandering how do I find that which  atom name mismatched. The 
forcefield folder is in my working directory and there are all files. 
atomtypes.atp is there and which contains the atom names  which I posted last 
email
Thanks for your regard
Hari



On Monday, October 28, 2013 4:50 PM, Justin Lemkul  wrote:
 


On 10/28/13 7:41 PM, Hari Pandey wrote:
>
>
>
>
> Thank you so much  Mark.
>
> I still did not understand. More detaily.  Atomtypes are only following:
>
> atomtypes.atp::
>
> H       1.00800 ;       polar H
> DUM        0.0 ;       dummy atom
> HAL1       1.008000 ;      alphatic proton
> HAL2       1.008000 ;      alphatic proton
> HAL3       1.008000 ;      alphatic proton
> CTL1       12.011000 ;     carbonyl C (acetic acid/methyl acetate);;;
> CTL1       12.011000 ;     sp3 carbon with 1 H (-CH1-)
> CTL2       12.011000 ;     carbon of methylene group (-CH2-)
> CTL3       12.011000 ;     carbon of methyl group (-CH3)
> OBL        15.999400 ;     acetic acid carboxyl oxygen (e. to protein OB)
> OCL        15.999400 ;     acetate oxygen
> OSL        15.999400 ;     ester oxygen
> O2L          15.999400 ;     Nucleic acid =O in phosphate or sulfate
> SL           32.06 ;     Sulfate sulfur
> NA           22.989770    ;     FOR  sodium ion
>
>
> MR.rtp:
>
> S            SL      1.3600          0
>          OS1     O2L     -0.6000         0
>          OS2     O2L     -0.6000         0
>          OS3     O2L     -0.6000         0
>          C1      CTL1    -0.1900         0
>          H1      HAL1    0.0900          0
>          C2      CTL2    -0.1800         1
>          H2      HAL2    0.0900          1
>          H3      HAL2    0.0900          1
>          C3      CL      0.6300          2 ;
>          O1      OBL     -0.5200         2
>          O2      OSL     -0.3400         2
>          C4      CTL2    -0.1800         3
>          H4      HAL2    0.0900          3
>          H5      HAL2    0.0900          3
>          C5      CTL1    -0.0900         4
>          H6      HAL1    0.0900          4
>          C6      CTL2    -0.1800         5
>          H7      HAL2    0.0900          5
>          H8      HAL2    0.0900          5
>          C7      CTL2    -0.1800         6
>          H9      HAL2    0.0900          6
>          H10     HAL2    0.0900          6
>          C8      CTL2    -0.1800         7
>          H11     HAL2    0.0900          7
>          H12     HAL2    0.0900          7
>          C9      CTL3    -0.2700         8
>          H13     HAL3    0.0900          8
>          H14     HAL3    0.0900          8
>          H15     HAL3    0.0900          8
>          C10     CTL2    -0.1800         9
>          H16     HAL2    0.0900          9
>          H17     HAL2    0.0900          9
>          C11     CTL3    -0.2700         10
>          H18     HAL3    0.0900          10
>          H19     HAL3    0.0900          10
>          H20     HAL3    0.0900          10
>          C12     CL      0.6300          11 ;
>          O3      OBL     -0.5200         11
>          O4      OSL     -0.3400         11
>          C13     CTL2    -0.1800         12
>          H21     HAL2    0.0900          12
>          H22     HAL2    0.0900          12
>          C14     CTL1    -0.0900         13
>          H23     HAL1    0.0900          13
>          C15     CTL2    -0.1800         14
>          H24     HAL2    0.0900          14
>          H25     HAL2    0.0900          14
>          C16     CTL2    -0.1800         15
>          H26     HAL2    0.0900          15
>          H27     HAL2    0.0900          15
>          C17     CTL2    -0.1800         16
>
>
> I have A.pdb and  I got A.gro  using this force field.
>
>
> Some part of  A.pdb::
>
> REMARK   Created:  Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007
> CRYST1     8.760   8.760   8.760  90.00  90.00  90.00 P1        1
> MODEL        1
> ATOM      1  S   AOT   151       6.864  -6.902   0.078  1.00  0.00
> ATOM      2  OS1 AOT   151       7.820  -5.791  -0.815  1.00  0.00
> ATOM      3  OS2 AOT   151       5.369  -7.134  -0.714  1.00  0.00
> ATOM      4  OS3 AOT   151       6.589  -6.277   1.657  1.00  0.00
> ATOM      5  C1  AOT   151       7.728  -8.482   0.196  1.00  0.00
> ATOM      6  H1  AOT   151       8.702  -8.326   0.676  1.00  0.00
> ATOM      7  C2  AOT   151       7.952  -8.937  -1.268  1.00  0.00
> ATOM      8  H2  AOT   151       7.067  -9.120  -1.697  1.00  0.00
> ATOM      9  H3  AOT   151       8.423  -8.212  -1.771  1.00  0.00
> ATOM     10  C3  AOT   151       6.874  -9.526   1.026  1.00  0.00
> ATOM     11  O1  AOT   151       6.661  -9.024   2.356  1.00  0.00
> ATOM     12  O2  AOT   151       7.505 -10.821   1.169  1.00  0.00
> ATOM     13  C4  AOT   151       6.679 -11.663   1.968  1.00  0.00
> ATOM     14  H4  AOT   151   

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Justin Lemkul]

On 10/28/13 7:41 PM, Hari Pandey wrote:





Thank you so much  Mark.

I still did not understand. More detaily.  Atomtypes are only following:

atomtypes.atp::

H   1.00800 ;   polar H
DUM0.0 ;   dummy atom
HAL1   1.008000 ;  alphatic proton
HAL2   1.008000 ;  alphatic proton
HAL3   1.008000 ;  alphatic proton
CTL1   12.011000 ; carbonyl C (acetic acid/methyl acetate);;;
CTL1   12.011000 ; sp3 carbon with 1 H (-CH1-)
CTL2   12.011000 ; carbon of methylene group (-CH2-)
CTL3   12.011000 ; carbon of methyl group (-CH3)
OBL15.999400 ; acetic acid carboxyl oxygen (e. to protein OB)
OCL15.999400 ; acetate oxygen
OSL15.999400 ; ester oxygen
O2L  15.999400 ; Nucleic acid =O in phosphate or sulfate
SL   32.06 ; Sulfate sulfur
NA   22.989770; FOR  sodium ion


MR.rtp:

SSL  1.3600  0
 OS1 O2L -0.6000 0
 OS2 O2L -0.6000 0
 OS3 O2L -0.6000 0
 C1  CTL1-0.1900 0
 H1  HAL10.0900  0
 C2  CTL2-0.1800 1
 H2  HAL20.0900  1
 H3  HAL20.0900  1
 C3  CL  0.6300  2 ;
 O1  OBL -0.5200 2
 O2  OSL -0.3400 2
 C4  CTL2-0.1800 3
 H4  HAL20.0900  3
 H5  HAL20.0900  3
 C5  CTL1-0.0900 4
 H6  HAL10.0900  4
 C6  CTL2-0.1800 5
 H7  HAL20.0900  5
 H8  HAL20.0900  5
 C7  CTL2-0.1800 6
 H9  HAL20.0900  6
 H10 HAL20.0900  6
 C8  CTL2-0.1800 7
 H11 HAL20.0900  7
 H12 HAL20.0900  7
 C9  CTL3-0.2700 8
 H13 HAL30.0900  8
 H14 HAL30.0900  8
 H15 HAL30.0900  8
 C10 CTL2-0.1800 9
 H16 HAL20.0900  9
 H17 HAL20.0900  9
 C11 CTL3-0.2700 10
 H18 HAL30.0900  10
 H19 HAL30.0900  10
 H20 HAL30.0900  10
 C12 CL  0.6300  11 ;
 O3  OBL -0.5200 11
 O4  OSL -0.3400 11
 C13 CTL2-0.1800 12
 H21 HAL20.0900  12
 H22 HAL20.0900  12
 C14 CTL1-0.0900 13
 H23 HAL10.0900  13
 C15 CTL2-0.1800 14
 H24 HAL20.0900  14
 H25 HAL20.0900  14
 C16 CTL2-0.1800 15
 H26 HAL20.0900  15
 H27 HAL20.0900  15
 C17 CTL2-0.1800 16


I have A.pdb and  I got A.gro  using this force field.


Some part of  A.pdb::

REMARK   Created:  Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007
CRYST1 8.760   8.760   8.760  90.00  90.00  90.00 P11
MODEL1
ATOM  1  S   AOT   151   6.864  -6.902   0.078  1.00  0.00
ATOM  2  OS1 AOT   151   7.820  -5.791  -0.815  1.00  0.00
ATOM  3  OS2 AOT   151   5.369  -7.134  -0.714  1.00  0.00
ATOM  4  OS3 AOT   151   6.589  -6.277   1.657  1.00  0.00
ATOM  5  C1  AOT   151   7.728  -8.482   0.196  1.00  0.00
ATOM  6  H1  AOT   151   8.702  -8.326   0.676  1.00  0.00
ATOM  7  C2  AOT   151   7.952  -8.937  -1.268  1.00  0.00
ATOM  8  H2  AOT   151   7.067  -9.120  -1.697  1.00  0.00
ATOM  9  H3  AOT   151   8.423  -8.212  -1.771  1.00  0.00
ATOM 10  C3  AOT   151   6.874  -9.526   1.026  1.00  0.00
ATOM 11  O1  AOT   151   6.661  -9.024   2.356  1.00  0.00
ATOM 12  O2  AOT   151   7.505 -10.821   1.169  1.00  0.00
ATOM 13  C4  AOT   151   6.679 -11.663   1.968  1.00  0.00
ATOM 14  H4  AOT   151   5.837 -11.877   1.473  1.00  0.00
ATOM 15  H5  AOT   151   6.454 -11.200   2.825  1.00  0.00
ATOM 16  C5  AOT   151   7.443 -12.948   2.264  1.00  0.00
ATOM 17  H6  AOT   151   8.370 -12.683   2.786  1.00  0.00
ATOM 18  C6  AOT   151   6.520 -13.788   3.227  1.00  0.00
ATOM 19  H7  AOT   151   5.703 -14.049   2.713  1.00  0.00
ATOM 20  H8  AOT   151   6.258 -13.205   3.996  1.00  0.00
ATOM 21  C7  AOT   151   7.156 -15.071   3.796  1.00  0.00
ATOM 22  H9  AOT   151   7.386 -15.690   3.045  1.00  0.00
ATOM 23  H10 AOT   151   7.987 -14.835   4.300  1.00  0.00
ATOM 

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Hari Pandey]

Thank you so much  Mark. 

I still did not understand. More detaily.  Atomtypes are only following:

atomtypes.atp::

H       1.00800 ;       polar H
DUM        0.0 ;       dummy atom
HAL1       1.008000 ;      alphatic proton
HAL2       1.008000 ;      alphatic proton
HAL3       1.008000 ;      alphatic proton
CTL1       12.011000 ;     carbonyl C (acetic acid/methyl acetate);;;
CTL1       12.011000 ;     sp3 carbon with 1 H (-CH1-)
CTL2       12.011000 ;     carbon of methylene group (-CH2-)
CTL3       12.011000 ;     carbon of methyl group (-CH3)
OBL        15.999400 ;     acetic acid carboxyl oxygen (e. to protein OB)
OCL        15.999400 ;     acetate oxygen
OSL        15.999400 ;     ester oxygen
O2L          15.999400 ;     Nucleic acid =O in phosphate or sulfate
SL           32.06 ;     Sulfate sulfur
NA           22.989770    ;     FOR  sodium ion 


MR.rtp:

S            SL      1.3600          0
        OS1     O2L     -0.6000         0
        OS2     O2L     -0.6000         0
        OS3     O2L     -0.6000         0
        C1      CTL1    -0.1900         0
        H1      HAL1    0.0900          0
        C2      CTL2    -0.1800         1
        H2      HAL2    0.0900          1
        H3      HAL2    0.0900          1
        C3      CL      0.6300          2 ;
        O1      OBL     -0.5200         2
        O2      OSL     -0.3400         2
        C4      CTL2    -0.1800         3
        H4      HAL2    0.0900          3
        H5      HAL2    0.0900          3
        C5      CTL1    -0.0900         4
        H6      HAL1    0.0900          4
        C6      CTL2    -0.1800         5
        H7      HAL2    0.0900          5
        H8      HAL2    0.0900          5
        C7      CTL2    -0.1800         6
        H9      HAL2    0.0900          6
        H10     HAL2    0.0900          6
        C8      CTL2    -0.1800         7
        H11     HAL2    0.0900          7
        H12     HAL2    0.0900          7
        C9      CTL3    -0.2700         8
        H13     HAL3    0.0900          8
        H14     HAL3    0.0900          8
        H15     HAL3    0.0900          8
        C10     CTL2    -0.1800         9
        H16     HAL2    0.0900          9
        H17     HAL2    0.0900          9
        C11     CTL3    -0.2700         10
        H18     HAL3    0.0900          10
        H19     HAL3    0.0900          10
        H20     HAL3    0.0900          10
        C12     CL      0.6300          11 ;
        O3      OBL     -0.5200         11
        O4      OSL     -0.3400         11
        C13     CTL2    -0.1800         12                                      
                           
        H21     HAL2    0.0900          12                                      
                           
        H22     HAL2    0.0900          12                                      
                           
        C14     CTL1    -0.0900         13                                      
                           
        H23     HAL1    0.0900          13                                      
                           
        C15     CTL2    -0.1800         14                                      
                           
        H24     HAL2    0.0900          14                                      
                           
        H25     HAL2    0.0900          14                                      
                           
        C16     CTL2    -0.1800         15                                      
                           
        H26     HAL2    0.0900          15                                      
                           
        H27     HAL2    0.0900          15                                      
                           
        C17     CTL2    -0.1800         16 


I have A.pdb and  I got A.gro  using this force field.


Some part of  A.pdb::

REMARK   Created:  Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007
CRYST1     8.760   8.760   8.760  90.00  90.00  90.00 P1        1
MODEL        1
ATOM      1  S   AOT   151       6.864  -6.902   0.078  1.00  0.00              
ATOM      2  OS1 AOT   151       7.820  -5.791  -0.815  1.00  0.00              
ATOM      3  OS2 AOT   151       5.369  -7.134  -0.714  1.00  0.00              
ATOM      4  OS3 AOT   151       6.589  -6.277   1.657  1.00  0.00   
ATOM      5  C1  AOT   151       7.728  -8.482   0.196  1.00  0.00 
ATOM      6  H1  AOT   151       8.702  -8.326   0.676  1.00  0.00
ATOM      7  C2  AOT   151       7.952  -8.937  -1.268  1.00  0.00
ATOM      8  H2  AOT   151       7.067  -9.120  -1.697  1.00  0.00              
ATOM      9  H3  AOT   151       8.423  -8.212  -1.771  1.00  0.00      
ATOM     10  C3  AOT   151       6.874  -9.526   1.026  1.00  0.00
ATOM     11  O1  AOT   151       6.661  -9.024   2.356  1.00  0.00 
ATOM     12  O2  AOT   151       7.505 -10.821   1.169  1.00  0.00  
ATOM     13  C4  AOT   151       6.679 

Re: [gmx-users] How can I increase maximum number of pulling step for energy minimization?

[Justin Lemkul]

On 10/28/13 1:59 PM, Gwonchan Yoon wrote:

Hi gromacs users:

I use gromacs 4.5.6 for energy minimization with steepest descent method
for ubiquitin pulling simulation with pulling step for applying
displacement. For that simulation, I should repeat pulling and minimization
process. I need 10^4 pulling step calculation to get fully unfolded
structure, but the calculation stops at 503 pulling step with follow error
message.


=
Source code file: futil.c, line: 489

File input/output error:
abc.edr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Sorry!  You were supposed to get help about:
 mpi-abort
But I couldn't open the help file:
 /usr/local/share/openmpi/help-mpi-api.txt: Too many open files.  Sorry!
--
=


I open the futil.c line: 489, and that line is as follows.


=
gmx_file(buf);
=


However, I cannot catch what should I change to that line.
If you have any ideas, please let me know.



You shouldn't change the source to get around the error.  There's nothing really 
that you can do there.


I/O errors happen when files cannot be read or written to, either because of 
permission problems, full disk, file system glitches, simulation crashing, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Mark Abraham]

On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey  wrote:

> Dear Gromacs Users,
>
> First, I would like to thank Dr. Lemkul for reply.
>
> My problem description is as follows:
> I am using CHARMM36  forcefield to equilibrate of AOT. when I add the mass
> of all atoms from topology, it gives me 444.5 which is correct but when I
> run the script
>

Justin asked you about your atom names, but somehow you have forgotten to
answer him :-)


>
> editconf -c  -f A.gro -o A.gro   -density 1000  -bt cubic -box  5 -d 0.1 .
>
>
> It  display incorrect value for mass of input.  The mass of input should
> be 444.5 . The out come of above script is:
>
> Volume: 125 nm^3, corresponds to roughly 56200 electrons
> No velocities found
> system size :  0.215  0.234  0.157 (nm)
> diameter:  0.287   (nm)
> center  :  2.500  2.500  2.500 (nm)
> box vectors :  5.000  5.000  5.000 (nm)
> box angles  :  90.00  90.00  90.00 (degrees)
> box volume  : 125.00   (nm^3)
>
> WARNING: masses and atomic (Van der Waals) radii will be determined
>  based on residue and atom names. These numbers can deviate
>  from the correct mass and radius of the atom type.
>

editconf only has a .gro file, so it does not know about any atom types, or
bonds, so it is not worth trying to write code to guess correctly whether
HG1 is the first hydrogen on the gamma carbon, or the first mercury, etc.
We do write a warning message, but sometimes people don't read them.

Mark


>
> Volume  of input 125 (nm^3)
> Massof input 967.25 (a.m.u.)
> Density of input 12.8493 (g/l)
> Scaling all box vectors by 0.234221
> new system size :  0.050  0.055  0.037
> shift   :  1.914  1.914  1.914 (nm)
> new center  :  2.500  2.500  2.500 (nm)
> new box vectors :  5.000  5.000  5.000 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  : 125.00(nm^3)
> Here we can see that mass of input is  967.25 which is far beyond the
> reality. this will cause error in density and all other mass dependent
> parameters.
>
> Please  help me how do I come over to this error
> Thank you so much for you kind help
>
> Hari
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Re: [gmx-users] mdrun cpt

[Mark Abraham]

On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty wrote:

> Mark,
>
> The problem with one .tpr file set for 100ns is that when job number (say)
> 4 hits the wall limit, it crashes and never gets a chance to submit the
> next job. So it's not really automated.
>

That's why I suggested -maxh, so you can have an orderly shutdown. (Though
if a job can get suspended, that won't always help, because mdrun can't
find out about the suspension...)

Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
> till job 4 ends.


Sure - read your PBS docs and find the environment variable to read so that
job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on
it. But don't tell your sysadmins where I live. ;-) Seriously, if you live
on this edge, you could spam infinite jobs, which tends to get your account
cut off. That's why you want the afterok hold - you only want the next job
to start if the exit code from the first script correctly indicates that
mdrun exited correctly. Test carefully!

Mark

But the PBS queuing system is sometime weird and takes a
> bit of time to recognize a job and give back its jobID. So I could submit
> job 5 but be unable to change its status to /hold/ because PBS does not
> return its ID. Another problem is that if resources are available, job 5
> could start before I ever get a chance to /hold/ it.
>
>
>
>
> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham  >wrote:
>
> > On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty  > >wrote:
> >
> > > I have need to collect 100ns but I can collect only ~1ns (1000steps)
> per
> > > run. Since I dont have .trr files, I rely on .cpt files for restarts.
> For
> > > example,
> > >
> > > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> > >
> > > This runs into a problem when the run gets killed due to walltime
> > limits. I
> > > now have a .xtc file which has run (say) 700 steps and a .cpt file
> which
> > > was last written at 600th step.
> > >
> >
> > You seem to have no need to use grompp, because you don't need to use a
> > workflow that generates multiple .tpr files. Do the equivalent of what
> the
> > restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
> .tpr
> > for the whole 100ns run, and then keep doing
> >
> > mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
> >
> > with or without -append, perhaps with -maxh, keeping whatever manual
> > backups you feel necessary. Then perhaps concatenate your final
> trajectory
> > files, according to your earlier choices.
> >
> > - To set up the next run I use the .cpt file from 600th step.
> > > - Now during analysis if I want to center the protein and such,
> /trjconv/
> > > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
> > know
> > > to stop at 600th step?
> >
> >
> > trjconv just operates on the contents of the trajectory file, as modified
> > by things like -b -e and -dt. The .tpr just gives it context, such as
> atom
> > names. You could give it a .tpr from any point during the run.
> >
> > Mark
> >
> > If this has to be put in manually, it becomes
> > > cumbersome.
> > >
> > > Thoughts?
> > >
> > >
> > >
> > >
> > >
> > > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul 
> wrote:
> > >
> > > >
> > > >
> > > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> > > >
> > > >> Hello All,
> > > >>
> > > >> Is there a way to make mdrun put out .cpt file with the same
> frequency
> > > as
> > > >> a
> > > >> .xtc or .trr file. From here
> > > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that
> > we
> > > >> can choose how often (time in mins) the .cpt file is written. But
> > > clearly
> > > >> if the frequency of output of .cpt (frequency in mins) and .xtc
> > > (frequency
> > > >> in simulation steps) do not match, it can create problems during
> > > analysis;
> > > >> especially in the event of frequent crashes. Also, I am not storing
> > .trr
> > > >> file since I dont need that precision.
> > > >> I am using Gromacs 4.6.1.
> > > >>
> > > >>
> > > > What problems are you experiencing?  There is no need for .cpt
> > frequency
> > > > to be the same as .xtc frequency, because any duplicate frames should
> > be
> > > > handled elegantly when appending.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==**
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 601
> > > > University of Maryland, Baltimore
> > > > 20 Penn St.
> > > > Baltimore, MD 21201
> > > >
> > > > jalemkul@outerbanks.umaryland.**edu <
> jalem...@outerbanks.umaryland.edu
> > >
> > > | (410)
> > > > 706-7441
> > > >
> > > > ==**
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://l

Re: [gmx-users] Failure in MD run without any error

[Mark Abraham]

Hi,

Hard to know. LAM was discontinued over 4 years ago. You could have a flaky
file system. Unless you're trying to run a jobsover both machines over
network like Infiniband, you don't even want to use an external MPI library
- single-node performance with built-in thread-MPI will give much better
value.

Mark


On Mon, Oct 28, 2013 at 9:12 PM, niloofar niknam
wrote:

>
>
>  DearGromacs users
> I have encountered something strange. I have installed Red
> Hat Enterprise Linux 6.1 & 6.2 on two machines recently and then lam 7.1.4,
> fftw 3.3.2 and Gromacs 4.5.5 .
> During linux installation, everything went well I didn`t
> face any complain or receiving any error, as well as in lam, fftw and
> Gromacs
> installation, But when I run an MD job on both of these machines, at first
> everything seems normal but after some steps ( usually multi thousands
> steps), the
> job doesn`t proceed. Log file does not show any change or there is no
> error.
> Obviously the job is stopped while terminal shows all the processors are
> 100%
> busy.
> I have also reinstalled the linux and the mentioned programs
> too but it did not solve the problem. I don`t have any idea what the
> problem
> is. Any comment or suggestion would be highly appreciated.
> Thanks in advance,
> Niloofar
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Obtaining trajectory coordinates at all dt

[Mark Abraham]

On Mon, Oct 28, 2013 at 7:56 PM, Xu Dong Huang wrote:

> Hello,
>
> I have couple objectives as part of an analysis of my simulated system.
> And I would like some opinions on the tools to use to achieve it.
>
> I have the following interest in my system:
> 1) Find the probability distribution (density) of bond angle on my
> molecule between (i.e atom 12, 2,3 , 13, etc) as a function of time step,
> essentially, the equilibrium angle. [would I use g_chi for such analysis? ]
>

Summary of available tools in manual 7.4 and 8 - good place to look first.
Probably you want g_angle.


> 2) I want the above result in an excel spreadsheet, is there a way to
> obtain it as a spreadsheet? Or I can only get a plot representation as a
> function of time?
>

http://www.gromacs.org/Documentation/How-tos/Graphing_Data

Mark


> Please share your expertise and opinions.
>
> Thank you.
>
> Xu Huang
>
>
> --
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Re: [gmx-users] Replica Exchange with Solute Tempering

[Andrew Ritchie]

Greetings,
I would also be interested in an example of using REST via Hamiltonian REMD
in the current gromacs build.  I'm particularly interested in enhanced
conformational sampling of 160-270 residue proteins. As it stands, I've
been unable to achieve any appreciable exchange probability in coulomb or
vdw lambdas without resorting to changing the lambda values by +/- 0.02 or
less and am hoping ST will allow me to increase the spacing between lambdas.
Thanks for any help,
Andrew


On Sat, Oct 26, 2013 at 9:45 PM, HANNIBAL LECTER  wrote:

> Hi
> I had tried using gromacs-4.6.1 to perform solute tempering. If you go
> through terakawa's paper you have to describe the lambdas corresponding to
> the temperatures. In your topology file define the params corresponding  to
> the two end states l=0 and l=1. Then define vdw, bonded and coulomb lambdas
> in the mdp file. The format is very well described in the manual. Then just
> the regular -replex syntax would perform solute tempering. However, the
> free energy module required to perform this, is extremely slow.
> On Oct 26, 2013 8:46 PM, "David Osguthorpe" 
> wrote:
>
> > On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote:
> > > Hi, all-
> > >
> > > Rest essentially scales the solute-solvent interactions, but maintains
> > > the solute-solute interactions. This can be done solely with
> > > Hamiltonian replica exchange, which is in 4.6.  It's a bit tricky,
> > > though.  We plan on having something that does this automatically in
> > > 5.0 or 5.1, but it's not there yet.
> > >
> > > What do you intend to do?  It could be that there's a better way to do
> > > what you want to do with Hamiltonian replica exchange, as well.
> > >
> >
> > Sorry - yes Im looking for an example of how to do REST via Hamiltonian
> > replica exchange
> >
> > Ive seen the papers by Moors (Improved Replica Exchange Method for
> > Native-State Protein Sampling)
> > and Terekawa (On easy implementation of a variant of the replica exchange
> > with solute tempering in GROMACS)
> > and followed some of the gromacs user list discussions from 2011 on REST
> > simulations
> >
> > As you say, it looks like its "a bit tricky" so was hoping there was a
> toy
> > example
> > somewhere
> >
> > Thanks
> >
> > David
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
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[gmx-users] Failure in MD run without any error

[niloofar niknam]

 DearGromacs users
I have encountered something strange. I have installed Red
Hat Enterprise Linux 6.1 & 6.2 on two machines recently and then lam 7.1.4,
fftw 3.3.2 and Gromacs 4.5.5 .
During linux installation, everything went well I didn`t
face any complain or receiving any error, as well as in lam, fftw and Gromacs
installation, But when I run an MD job on both of these machines, at first
everything seems normal but after some steps ( usually multi thousands steps), 
the
job doesn`t proceed. Log file does not show any change or there is no error.
Obviously the job is stopped while terminal shows all the processors are 100%
busy.
I have also reinstalled the linux and the mentioned programs
too but it did not solve the problem. I don`t have any idea what the problem
is. Any comment or suggestion would be highly appreciated.
Thanks in advance,
Niloofar

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Re: [gmx-users] mdrun cpt

[jkrieger]

You're welcome

On 28 Oct 2013, at 20:03, Pavan Ghatty  wrote:

> Aah yes of course. Thanks James.
> 
> 
> 
> On Mon, Oct 28, 2013 at 3:16 PM,  wrote:
> 
>> No this isn't a problem. You can use job names under the -hold_jid flag.
>> As long as you change the job name in the submit script between
>> submissions this isn't a problem. You could have a submit script for job 4
>> with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
>> -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as
>> you have made this change which will be within seconds of submitting job
>> 4.
>> 
>>> Mark,
>>> 
>>> The problem with one .tpr file set for 100ns is that when job number
>> (say)
>>> 4 hits the wall limit, it crashes and never gets a chance to submit the
>>> next job. So it's not really automated.
>>> 
>>> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job
>> 5
>>> till job 4 ends. But the PBS queuing system is sometime weird and takes a
>>> bit of time to recognize a job and give back its jobID. So I could submit
>>> job 5 but be unable to change its status to /hold/ because PBS does not
>>> return its ID. Another problem is that if resources are available, job 5
>>> could start before I ever get a chance to /hold/ it.
>>> 
>>> 
>>> 
>>> 
>>> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham
>>> wrote:
>>> 
 On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty  wrote:
 
> I have need to collect 100ns but I can collect only ~1ns (1000steps)
 per
> run. Since I dont have .trr files, I rely on .cpt files for restarts.
 For
> example,
> 
> grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> 
> This runs into a problem when the run gets killed due to walltime
 limits. I
> now have a .xtc file which has run (say) 700 steps and a .cpt file
 which
> was last written at 600th step.
 
 You seem to have no need to use grompp, because you don't need to use a
 workflow that generates multiple .tpr files. Do the equivalent of what
 the
 restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
 .tpr
 for the whole 100ns run, and then keep doing
 
 mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
 
 with or without -append, perhaps with -maxh, keeping whatever manual
 backups you feel necessary. Then perhaps concatenate your final
 trajectory
 files, according to your earlier choices.
 
 - To set up the next run I use the .cpt file from 600th step.
> - Now during analysis if I want to center the protein and such,
 /trjconv/
> needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
 know
> to stop at 600th step?
 
 
 trjconv just operates on the contents of the trajectory file, as
 modified
 by things like -b -e and -dt. The .tpr just gives it context, such as
 atom
 names. You could give it a .tpr from any point during the run.
 
 Mark
 
 If this has to be put in manually, it becomes
> cumbersome.
> 
> Thoughts?
> 
> 
> 
> 
> 
> On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul 
 wrote:
> 
>> 
>> 
>> On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>> 
>>> Hello All,
>>> 
>>> Is there a way to make mdrun put out .cpt file with the same
 frequency
> as
>>> a
>>> .xtc or .trr file. From here
>>> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see
>> that
 we
>>> can choose how often (time in mins) the .cpt file is written. But
> clearly
>>> if the frequency of output of .cpt (frequency in mins) and .xtc
> (frequency
>>> in simulation steps) do not match, it can create problems during
> analysis;
>>> especially in the event of frequent crashes. Also, I am not storing
 .trr
>>> file since I dont need that precision.
>>> I am using Gromacs 4.6.1.
>> What problems are you experiencing?  There is no need for .cpt
 frequency
>> to be the same as .xtc frequency, because any duplicate frames
 should
 be
>> handled elegantly when appending.
>> 
>> -Justin
>> 
>> --
>> ==**
>> 
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalemkul@outerbanks.umaryland.**edu
  
> | (410)
>> 706-7441
>> 
>> ==**
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.

Re: [gmx-users] mdrun cpt

[Pavan Ghatty]

Aah yes of course. Thanks James.



On Mon, Oct 28, 2013 at 3:16 PM,  wrote:

> No this isn't a problem. You can use job names under the -hold_jid flag.
> As long as you change the job name in the submit script between
> submissions this isn't a problem. You could have a submit script for job 4
> with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
> -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as
> you have made this change which will be within seconds of submitting job
> 4.
>
> > Mark,
> >
> > The problem with one .tpr file set for 100ns is that when job number
> (say)
> > 4 hits the wall limit, it crashes and never gets a chance to submit the
> > next job. So it's not really automated.
> >
> > Now I could initiate job 5 before /mdrun/ in job 4's script and hold job
> 5
> > till job 4 ends. But the PBS queuing system is sometime weird and takes a
> > bit of time to recognize a job and give back its jobID. So I could submit
> > job 5 but be unable to change its status to /hold/ because PBS does not
> > return its ID. Another problem is that if resources are available, job 5
> > could start before I ever get a chance to /hold/ it.
> >
> >
> >
> >
> > On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham
> > wrote:
> >
> >> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty  >> >wrote:
> >>
> >> > I have need to collect 100ns but I can collect only ~1ns (1000steps)
> >> per
> >> > run. Since I dont have .trr files, I rely on .cpt files for restarts.
> >> For
> >> > example,
> >> >
> >> > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> >> >
> >> > This runs into a problem when the run gets killed due to walltime
> >> limits. I
> >> > now have a .xtc file which has run (say) 700 steps and a .cpt file
> >> which
> >> > was last written at 600th step.
> >> >
> >>
> >> You seem to have no need to use grompp, because you don't need to use a
> >> workflow that generates multiple .tpr files. Do the equivalent of what
> >> the
> >> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
> >> .tpr
> >> for the whole 100ns run, and then keep doing
> >>
> >> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
> >>
> >> with or without -append, perhaps with -maxh, keeping whatever manual
> >> backups you feel necessary. Then perhaps concatenate your final
> >> trajectory
> >> files, according to your earlier choices.
> >>
> >> - To set up the next run I use the .cpt file from 600th step.
> >> > - Now during analysis if I want to center the protein and such,
> >> /trjconv/
> >> > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
> >> know
> >> > to stop at 600th step?
> >>
> >>
> >> trjconv just operates on the contents of the trajectory file, as
> >> modified
> >> by things like -b -e and -dt. The .tpr just gives it context, such as
> >> atom
> >> names. You could give it a .tpr from any point during the run.
> >>
> >> Mark
> >>
> >> If this has to be put in manually, it becomes
> >> > cumbersome.
> >> >
> >> > Thoughts?
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul 
> >> wrote:
> >> >
> >> > >
> >> > >
> >> > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> >> > >
> >> > >> Hello All,
> >> > >>
> >> > >> Is there a way to make mdrun put out .cpt file with the same
> >> frequency
> >> > as
> >> > >> a
> >> > >> .xtc or .trr file. From here
> >> > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> >> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see
> that
> >> we
> >> > >> can choose how often (time in mins) the .cpt file is written. But
> >> > clearly
> >> > >> if the frequency of output of .cpt (frequency in mins) and .xtc
> >> > (frequency
> >> > >> in simulation steps) do not match, it can create problems during
> >> > analysis;
> >> > >> especially in the event of frequent crashes. Also, I am not storing
> >> .trr
> >> > >> file since I dont need that precision.
> >> > >> I am using Gromacs 4.6.1.
> >> > >>
> >> > >>
> >> > > What problems are you experiencing?  There is no need for .cpt
> >> frequency
> >> > > to be the same as .xtc frequency, because any duplicate frames
> >> should
> >> be
> >> > > handled elegantly when appending.
> >> > >
> >> > > -Justin
> >> > >
> >> > > --
> >> > > ==**
> >> > >
> >> > > Justin A. Lemkul, Ph.D.
> >> > > Postdoctoral Fellow
> >> > >
> >> > > Department of Pharmaceutical Sciences
> >> > > School of Pharmacy
> >> > > Health Sciences Facility II, Room 601
> >> > > University of Maryland, Baltimore
> >> > > 20 Penn St.
> >> > > Baltimore, MD 21201
> >> > >
> >> > > jalemkul@outerbanks.umaryland.**edu
> >>  >> >
> >> > | (410)
> >> > > 706-7441
> >> > >
> >> > > ==**
> >> > > --
> >> > > gmx-users mailing listgmx-users@gromacs.org
> >> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> >

Re: [gmx-users] mdrun cpt

[jkrieger]

No this isn't a problem. You can use job names under the -hold_jid flag.
As long as you change the job name in the submit script between
submissions this isn't a problem. You could have a submit script for job 4
with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and
-hold_jid md_job4 for the next job. Then you can submit job 5 as soon as
you have made this change which will be within seconds of submitting job
4.

> Mark,
>
> The problem with one .tpr file set for 100ns is that when job number (say)
> 4 hits the wall limit, it crashes and never gets a chance to submit the
> next job. So it's not really automated.
>
> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
> till job 4 ends. But the PBS queuing system is sometime weird and takes a
> bit of time to recognize a job and give back its jobID. So I could submit
> job 5 but be unable to change its status to /hold/ because PBS does not
> return its ID. Another problem is that if resources are available, job 5
> could start before I ever get a chance to /hold/ it.
>
>
>
>
> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham
> wrote:
>
>> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty > >wrote:
>>
>> > I have need to collect 100ns but I can collect only ~1ns (1000steps)
>> per
>> > run. Since I dont have .trr files, I rely on .cpt files for restarts.
>> For
>> > example,
>> >
>> > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
>> >
>> > This runs into a problem when the run gets killed due to walltime
>> limits. I
>> > now have a .xtc file which has run (say) 700 steps and a .cpt file
>> which
>> > was last written at 600th step.
>> >
>>
>> You seem to have no need to use grompp, because you don't need to use a
>> workflow that generates multiple .tpr files. Do the equivalent of what
>> the
>> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a
>> .tpr
>> for the whole 100ns run, and then keep doing
>>
>> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
>>
>> with or without -append, perhaps with -maxh, keeping whatever manual
>> backups you feel necessary. Then perhaps concatenate your final
>> trajectory
>> files, according to your earlier choices.
>>
>> - To set up the next run I use the .cpt file from 600th step.
>> > - Now during analysis if I want to center the protein and such,
>> /trjconv/
>> > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
>> know
>> > to stop at 600th step?
>>
>>
>> trjconv just operates on the contents of the trajectory file, as
>> modified
>> by things like -b -e and -dt. The .tpr just gives it context, such as
>> atom
>> names. You could give it a .tpr from any point during the run.
>>
>> Mark
>>
>> If this has to be put in manually, it becomes
>> > cumbersome.
>> >
>> > Thoughts?
>> >
>> >
>> >
>> >
>> >
>> > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul 
>> wrote:
>> >
>> > >
>> > >
>> > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>> > >
>> > >> Hello All,
>> > >>
>> > >> Is there a way to make mdrun put out .cpt file with the same
>> frequency
>> > as
>> > >> a
>> > >> .xtc or .trr file. From here
>> > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
>> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that
>> we
>> > >> can choose how often (time in mins) the .cpt file is written. But
>> > clearly
>> > >> if the frequency of output of .cpt (frequency in mins) and .xtc
>> > (frequency
>> > >> in simulation steps) do not match, it can create problems during
>> > analysis;
>> > >> especially in the event of frequent crashes. Also, I am not storing
>> .trr
>> > >> file since I dont need that precision.
>> > >> I am using Gromacs 4.6.1.
>> > >>
>> > >>
>> > > What problems are you experiencing?  There is no need for .cpt
>> frequency
>> > > to be the same as .xtc frequency, because any duplicate frames
>> should
>> be
>> > > handled elegantly when appending.
>> > >
>> > > -Justin
>> > >
>> > > --
>> > > ==**
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Postdoctoral Fellow
>> > >
>> > > Department of Pharmaceutical Sciences
>> > > School of Pharmacy
>> > > Health Sciences Facility II, Room 601
>> > > University of Maryland, Baltimore
>> > > 20 Penn St.
>> > > Baltimore, MD 21201
>> > >
>> > > jalemkul@outerbanks.umaryland.**edu
>> > >
>> > | (410)
>> > > 706-7441
>> > >
>> > > ==**
>> > > --
>> > > gmx-users mailing listgmx-users@gromacs.org
>> > > 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>before posting!
>> > > * Please don't post (un)subscribe requests to the list. Use the www
>> > > interface or send it to gmx-users-requ...@gromacs.org.
>> > > 

[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Hari Pandey]

Dear Gromacs Users,

First, I would like to thank Dr. Lemkul for reply.

My problem description is as follows:
I am using CHARMM36  forcefield to equilibrate of AOT. when I add the mass of 
all atoms from topology, it gives me 444.5 which is correct but when I run the 
script

editconf -c  -f A.gro -o A.gro   -density 1000  -bt cubic -box  5 -d 0.1 .


It  display incorrect value for mass of input.  The mass of input should be 
444.5 . The out come of above script is:

Volume: 125 nm^3, corresponds to roughly 56200 electrons
No velocities found
    system size :  0.215  0.234  0.157 (nm)
    diameter    :  0.287               (nm)
    center      :  2.500  2.500  2.500 (nm)
    box vectors :  5.000  5.000  5.000 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 125.00               (nm^3)

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Volume  of input 125 (nm^3)
Mass    of input 967.25 (a.m.u.)
Density of input 12.8493 (g/l)
Scaling all box vectors by 0.234221
new system size :  0.050  0.055  0.037
    shift       :  1.914  1.914  1.914 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00(nm^3)
Here we can see that mass of input is  967.25 which is far beyond the reality. 
this will cause error in density and all other mass dependent parameters. 

Please  help me how do I come over to this error
Thank you so much for you kind help

Hari
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[gmx-users] Obtaining trajectory coordinates at all dt

[Xu Dong Huang]

Hello,

I have couple objectives as part of an analysis of my simulated system. And I 
would like some opinions on the tools to use to achieve it. 

I have the following interest in my system:
1) Find the probability distribution (density) of bond angle on my molecule 
between (i.e atom 12, 2,3 , 13, etc) as a function of time step, essentially, 
the equilibrium angle. [would I use g_chi for such analysis? ]
2) I want the above result in an excel spreadsheet, is there a way to obtain it 
as a spreadsheet? Or I can only get a plot representation as a function of time?

Please share your expertise and opinions. 

Thank you. 

Xu Huang


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Re: [gmx-users] mdrun cpt

[Pavan Ghatty]

Mark,

The problem with one .tpr file set for 100ns is that when job number (say)
4 hits the wall limit, it crashes and never gets a chance to submit the
next job. So it's not really automated.

Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5
till job 4 ends. But the PBS queuing system is sometime weird and takes a
bit of time to recognize a job and give back its jobID. So I could submit
job 5 but be unable to change its status to /hold/ because PBS does not
return its ID. Another problem is that if resources are available, job 5
could start before I ever get a chance to /hold/ it.




On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham wrote:

> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty  >wrote:
>
> > I have need to collect 100ns but I can collect only ~1ns (1000steps) per
> > run. Since I dont have .trr files, I rely on .cpt files for restarts. For
> > example,
> >
> > grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
> >
> > This runs into a problem when the run gets killed due to walltime
> limits. I
> > now have a .xtc file which has run (say) 700 steps and a .cpt file which
> > was last written at 600th step.
> >
>
> You seem to have no need to use grompp, because you don't need to use a
> workflow that generates multiple .tpr files. Do the equivalent of what the
> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr
> for the whole 100ns run, and then keep doing
>
> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime
>
> with or without -append, perhaps with -maxh, keeping whatever manual
> backups you feel necessary. Then perhaps concatenate your final trajectory
> files, according to your earlier choices.
>
> - To set up the next run I use the .cpt file from 600th step.
> > - Now during analysis if I want to center the protein and such, /trjconv/
> > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/
> know
> > to stop at 600th step?
>
>
> trjconv just operates on the contents of the trajectory file, as modified
> by things like -b -e and -dt. The .tpr just gives it context, such as atom
> names. You could give it a .tpr from any point during the run.
>
> Mark
>
> If this has to be put in manually, it becomes
> > cumbersome.
> >
> > Thoughts?
> >
> >
> >
> >
> >
> > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> > >
> > >> Hello All,
> > >>
> > >> Is there a way to make mdrun put out .cpt file with the same frequency
> > as
> > >> a
> > >> .xtc or .trr file. From here
> > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that
> we
> > >> can choose how often (time in mins) the .cpt file is written. But
> > clearly
> > >> if the frequency of output of .cpt (frequency in mins) and .xtc
> > (frequency
> > >> in simulation steps) do not match, it can create problems during
> > analysis;
> > >> especially in the event of frequent crashes. Also, I am not storing
> .trr
> > >> file since I dont need that precision.
> > >> I am using Gromacs 4.6.1.
> > >>
> > >>
> > > What problems are you experiencing?  There is no need for .cpt
> frequency
> > > to be the same as .xtc frequency, because any duplicate frames should
> be
> > > handled elegantly when appending.
> > >
> > > -Justin
> > >
> > > --
> > > ==**
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul@outerbanks.umaryland.**edu  >
> > | (410)
> > > 706-7441
> > >
> > > ==**
> > > --
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> > > 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/**
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> http://lists.

[gmx-users] How can I increase maximum number of pulling step for energy minimization?

[Gwonchan Yoon]

Hi gromacs users:

I use gromacs 4.5.6 for energy minimization with steepest descent method
for ubiquitin pulling simulation with pulling step for applying
displacement. For that simulation, I should repeat pulling and minimization
process. I need 10^4 pulling step calculation to get fully unfolded
structure, but the calculation stops at 503 pulling step with follow error
message.


=
Source code file: futil.c, line: 489

File input/output error:
abc.edr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Sorry!  You were supposed to get help about:
mpi-abort
But I couldn't open the help file:
/usr/local/share/openmpi/help-mpi-api.txt: Too many open files.  Sorry!
--
=


I open the futil.c line: 489, and that line is as follows.


=
gmx_file(buf);
=


However, I cannot catch what should I change to that line.
If you have any ideas, please let me know.

Sincerely,

Chan
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Re: [gmx-users] parmbsc0 force field

[Justin Lemkul]

On 10/28/13 10:06 AM, kiana moghaddam wrote:

Hi GMX users
I want to use parmbsc0 force field for G-quadruplex structures MD simulation, but I'm 
not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs 
site(http://www.gromacs.org/Special:Search?search=parmbsc0&ns=main&path=) is 
the parmbsc0 force field.


Based on the name, it probably is.  Check its contents against the relevant 
literature to be sure (minding unit conversion, of course).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] mdrun cpt

[Mark Abraham]

On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty wrote:

> I have need to collect 100ns but I can collect only ~1ns (1000steps) per
> run. Since I dont have .trr files, I rely on .cpt files for restarts. For
> example,
>
> grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15
>
> This runs into a problem when the run gets killed due to walltime limits. I
> now have a .xtc file which has run (say) 700 steps and a .cpt file which
> was last written at 600th step.
>

You seem to have no need to use grompp, because you don't need to use a
workflow that generates multiple .tpr files. Do the equivalent of what the
restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr
for the whole 100ns run, and then keep doing

mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime

with or without -append, perhaps with -maxh, keeping whatever manual
backups you feel necessary. Then perhaps concatenate your final trajectory
files, according to your earlier choices.

- To set up the next run I use the .cpt file from 600th step.
> - Now during analysis if I want to center the protein and such, /trjconv/
> needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know
> to stop at 600th step?


trjconv just operates on the contents of the trajectory file, as modified
by things like -b -e and -dt. The .tpr just gives it context, such as atom
names. You could give it a .tpr from any point during the run.

Mark

If this has to be put in manually, it becomes
> cumbersome.
>
> Thoughts?
>
>
>
>
>
> On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 10/27/13 9:37 AM, Pavan Ghatty wrote:
> >
> >> Hello All,
> >>
> >> Is there a way to make mdrun put out .cpt file with the same frequency
> as
> >> a
> >> .xtc or .trr file. From here
> >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that we
> >> can choose how often (time in mins) the .cpt file is written. But
> clearly
> >> if the frequency of output of .cpt (frequency in mins) and .xtc
> (frequency
> >> in simulation steps) do not match, it can create problems during
> analysis;
> >> especially in the event of frequent crashes. Also, I am not storing .trr
> >> file since I dont need that precision.
> >> I am using Gromacs 4.6.1.
> >>
> >>
> > What problems are you experiencing?  There is no need for .cpt frequency
> > to be the same as .xtc frequency, because any duplicate frames should be
> > handled elegantly when appending.
> >
> > -Justin
> >
> > --
> > ==**
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul@outerbanks.umaryland.**edu 
> | (410)
> > 706-7441
> >
> > ==**
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > 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<
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Re: [gmx-users] mdrun cpt

[Pavan Ghatty]

I have need to collect 100ns but I can collect only ~1ns (1000steps) per
run. Since I dont have .trr files, I rely on .cpt files for restarts. For
example,

grompp -f md.mdp  -c md_14.gro -t md_14.cpt -p system.top -o md_15

This runs into a problem when the run gets killed due to walltime limits. I
now have a .xtc file which has run (say) 700 steps and a .cpt file which
was last written at 600th step.
- To set up the next run I use the .cpt file from 600th step.
- Now during analysis if I want to center the protein and such, /trjconv/
needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know
to stop at 600th step? If this has to be put in manually, it becomes
cumbersome.

Thoughts?





On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul  wrote:

>
>
> On 10/27/13 9:37 AM, Pavan Ghatty wrote:
>
>> Hello All,
>>
>> Is there a way to make mdrun put out .cpt file with the same frequency as
>> a
>> .xtc or .trr file. From here
>> http://www.gromacs.org/**Documentation/How-tos/Doing_**RestartsI
>>  see that we
>> can choose how often (time in mins) the .cpt file is written. But clearly
>> if the frequency of output of .cpt (frequency in mins) and .xtc (frequency
>> in simulation steps) do not match, it can create problems during analysis;
>> especially in the event of frequent crashes. Also, I am not storing .trr
>> file since I dont need that precision.
>> I am using Gromacs 4.6.1.
>>
>>
> What problems are you experiencing?  There is no need for .cpt frequency
> to be the same as .xtc frequency, because any duplicate frames should be
> handled elegantly when appending.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
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[gmx-users] parmbsc0 force field

[kiana moghaddam]

Hi GMX users
I want to use parmbsc0 force field for G-quadruplex structures MD simulation, 
but I'm not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs 
site(http://www.gromacs.org/Special:Search?search=parmbsc0&ns=main&path=) is 
the parmbsc0 force field.
Please help me
Sincerely
Kiana 
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[gmx-users] Suggestion for a project

[Asaf Farhi]

Dear Gromacs Users

I would like to suggest a project in free energy calculations which can be in 
cooperation.
The project is to demonstrate a novel and interesting method to calculate free 
energy differences between two solvation/binding processes.
The first simulations are rather simple (solvation) and it can be extended to 
(binding) and to demonstrating more theoretical parts.
The requirements are experience in MD simulations and alchemical 
transformations and immediate availability.
An experience in writing an article is an advantage.
To my opinion the demonstrations is likely to lead to an article or to be 
combined with existing material into an article. 
Information on the method can be found at:
http://arxiv.org/abs/1310.2112

People that are interested can contact me in the follwoing emails:
asaf.fa...@weizmann.ac.il
asaf.fa...@gmail.com

Thanks,
Best regards,
Asaf--
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[gmx-users] PLUMED2 official release

[Carlo Camilloni]

Dear GROMACS users and developers, 

We are very pleased to announce that PLUMED2 is available at 
www.plumed-code.org.

Version 2.0 is a complete rewrite, so there is no way to write a complete set 
of differences with respect to PLUMED. 
Here is a summary of the major differences:
- The input is simpler and more error proof. Many checks are now performed in 
such a way that common errors are avoided. 
- The units are now the same for all MD codes.  If you want to use different 
units than the default ones, you can now set them in the input file. 
- The analysis tools are now much more flexible.  As an example of this it is 
now possible to write different collective variables with different frequencies 
- Many complex collective variables are considerably faster with respect to 
PLUMED1. In particular, all variables based on RMSD distances. 
- Centers of mass can be used as if they were atoms. Hence, unlike PLUMED1, you 
can use center of mass positions in ALL collective variables.
- The virial contribution is now computed and passed to the MD code.  Plumed 
can thus now be used to perform biased NPT simulations 

In addition, it is now much easier to contribute new functionality to the code 
because: 
- There is a much simpler interface between PLUMED and the MD codes. This makes 
it much easier to add PLUMED to a new MD code. 
- PLUMED2 is written in a C++ object oriented programming and it is fully 
compatible with the C++ standard library 
- PLUMED2 is based on a modular structure 
- An extensive developer and user documentations are provided with the code

While PLUMED2 includes many more functionalities with respect to PLUMED1, some 
other are missing and will be implemented shortly.
Check the User manual in the How tos section about how moving from PLUMED1 to 
PLUMED2.

More information can be found in the PLUMED2 paper, available on arxiv:

http://arxiv.org/abs/1310.0980

and on the Computer Physics Communications website:

http://www.sciencedirect.com/science/article/pii/S0010465513003196

The PLUMED developers team.--
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Re: [gmx-users] Gromacs tutorials for binding free energy analysis

[Justin Lemkul]

On 10/28/13 8:02 AM, Sajad Ahrari wrote:

Hello dears
I would liked to know which of the tutorials presented by Gromacs for binding 
free energy analysis (http://www.gromacs.org/Documentation/Tutorials)  are 
based on LIE method?


I would suggest you read them and see.  I suspect none of them are, though.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Gromacs tutorials for binding free energy analysis

[Sajad Ahrari]

Hello dears
I would liked to know which of the tutorials presented by Gromacs for binding 
free energy analysis (http://www.gromacs.org/Documentation/Tutorials)  are 
based on LIE method?
regards,
Sajad

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Re: [gmx-users] Charges in vacuum simulation

[Dr. Vitaly Chaban]

If in vacuum, I would add hydrogens via covalent bonds.

Dr. Vitaly V. Chaban


On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh
 wrote:
> Hi all,
>
> I'm trying to run a vacuum simulation of my protein which has a non-zero 
> charge.
> How to deal with this charge? Can I add counter ions in to my system?
> Would it be energetically stable?
>
> How can one bring a protein to its isoelectric point?
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Re: [gmx-users] pdb2gmx conversion

[Tsjerk Wassenaar]

Hi Musyoka,

I would guess that that is related to the input coordinates. A bit of EM
should fix it.

Cheers,

Tsjerk


On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS <
mutemibiochemis...@gmail.com> wrote:

> Dear Users,
>
> Whenever i convert a protein.pdb file using the following command (pdb2gmx
> -f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the
> output with either vmd or pymol, i get the first amino acid residue
> breaking from the main chain.
>
> Would anyone help me understand why this is happening?
>
> Thanks.
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] pdb2gmx conversion

[MUSYOKA THOMMAS]

Dear Users,

Whenever i convert a protein.pdb file using the following command (pdb2gmx
-f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the
output with either vmd or pymol, i get the first amino acid residue
breaking from the main chain.

Would anyone help me understand why this is happening?

Thanks.
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Re: [gmx-users] g_hbond and g_rdf in vacuum

[Justin Lemkul]

On 10/28/13 3:30 AM, Santu Biswas wrote:

"Not working" is too vague a symptom for anyone to guess what the

problem

is, sorry.

Mark
On Oct 24, 2013 9:39 AM, "Santu Biswas" 

wrote:



dear users,

   I am performing 500ps mdrun in vacuum for

polypeptide(formed

by 10-residues leucine) using gromacs_4.5.5(double-

precision) using

opls-aa/L force field.Input file for 500ps mdrun is given below


title= peptide in vaccum
cpp= /lib/cpp

; RUN CONTROL
integrator = md
comm_mode= ANGULAR
nsteps = 50
dt= 0.001
; NEIGHBOR SEARCHING
nstlist  = 0
ns_type   = simple
pbc = no
rlist = 0
; OUTPUT CONTROL
nstxout  = 1000
nstvout  = 1000
nstxtcout   = 0
nstlog= 1000
constraints = none
nstenergy   = 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb = 0
; Method for doing Van der Waals
rvdw= 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl  = V-rescale
tc_grps= Protein
tau_t= 0.1
ref_t = 300
gen_vel= yes
gen_temp = 300

Using the 500ps trajectory if i run g_hbond_d for calculating the

number

of

hydrogen bonds as a function of time using index file(where atom O and

atom

N H is used) it is not working.
Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is

also

not working.
I do not know why this is happening.

--
santu
--

Thanks Mark for your reply.



Using the 500ps trajectory i want to calculate the number of hydrogen
bonds as a function of time in vacuum .For this calculation i


  have uesd
g_hbond_d  -f  traj_0-500ps.trr  -s 500ps.tpr -n index.ndx -num
hbond-num.xvg -dist dist.xvg -ang angle.xvg




With what groups? Can there be any hydrogen bonds between those groups?

Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a
shorter trajectory work because it took less time? Does doing only one of
three analyses help things to work? You'd be much closer to a solution if
you'd tried some simplifications and done some detective work already ;-)



Programm was running .After 1 hour it was still running but there was no
output.



 If I calculate the number of hydrogen bonds as a function of time in
water (no vacuum) using the same command line then there was  no problem.

Same problem when I used g_rdf in vacuum.The commad line I have used
g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also
checked with -nopbc with the same command line.




RDF of what, in vacuum? What groups did you use?



The programm is running but in the output file nothing is written.
If I used g_rdf in water using the same command line there was no
problem.



OK - but does your analysis make sense in vacuum?

Mark

Thanks Mark for your reply


In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I
want to calculate the distance between O atom and N-H hydrogen atom using
g_rdf in vacuum.


Similarly using the same index file I want to calculate the number of
hydrogen bonds as a function of time in vacuum using g_hbond.
Yes there is a H bond between C=O oxygen atom of i-th residue and N-H
hydrogen of i+4-th residue.
  I also checked with shorter trajectory there is also same problem .

Please let me know If there are any mistakes.



Does your system have a non-zero size?  That is, are all the box vectors a 
somewhat reasonable value?  They are, of course, irrelevant for the simulation 
(assuming pbc = no for in vacuo), but for analysis, you need a sensible box.  If 
you don't, you can recenter the trajectory using trjconv -box -center.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Charges in vacuum simulation

[Richa Singh]

Hi all,

I'm trying to run a vacuum simulation of my protein which has a non-zero charge.
How to deal with this charge? Can I add counter ions in to my system?
Would it be energetically stable?

How can one bring a protein to its isoelectric point?
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[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75

[Santu Biswas]

> > "Not working" is too vague a symptom for anyone to guess what the
problem
> > is, sorry.
> >
> > Mark
> > On Oct 24, 2013 9:39 AM, "Santu Biswas" 
> wrote:
> >
> > > dear users,
> > >
> > >   I am performing 500ps mdrun in vacuum for
> > polypeptide(formed
> > > by 10-residues leucine) using gromacs_4.5.5(double-
precision) using
> > > opls-aa/L force field.Input file for 500ps mdrun is given below
> > >
> > >
> > > title= peptide in vaccum
> > > cpp= /lib/cpp
> > >
> > > ; RUN CONTROL
> > > integrator = md
> > > comm_mode= ANGULAR
> > > nsteps = 50
> > > dt= 0.001
> > > ; NEIGHBOR SEARCHING
> > > nstlist  = 0
> > > ns_type   = simple
> > > pbc = no
> > > rlist = 0
> > > ; OUTPUT CONTROL
> > > nstxout  = 1000
> > > nstvout  = 1000
> > > nstxtcout   = 0
> > > nstlog= 1000
> > > constraints = none
> > > nstenergy   = 1000
> > > ; OPTION FOR ELECTROSTATIC AND VDW
> > > rcoulomb = 0
> > > ; Method for doing Van der Waals
> > > rvdw= 0
> > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > > tcoupl  = V-rescale
> > > tc_grps= Protein
> > > tau_t= 0.1
> > > ref_t = 300
> > > gen_vel= yes
> > > gen_temp = 300
> > >
> > > Using the 500ps trajectory if i run g_hbond_d for calculating the
> number
> > of
> > > hydrogen bonds as a function of time using index file(where atom O and
> > atom
> > > N H is used) it is not working.
> > > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is
> also
> > > not working.
> > > I do not know why this is happening.
> > >
> > > --
> > > santu
> > > --
> > Thanks Mark for your reply.
> >
>
>Using the 500ps trajectory i want to calculate the number of hydrogen
> bonds as a function of time in vacuum .For this calculation i
>
> >  have uesd
> > g_hbond_d  -f  traj_0-500ps.trr  -s 500ps.tpr -n index.ndx -num
> > hbond-num.xvg -dist dist.xvg -ang angle.xvg
>
>
With what groups? Can there be any hydrogen bonds between those groups?

Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a
shorter trajectory work because it took less time? Does doing only one of
three analyses help things to work? You'd be much closer to a solution if
you'd tried some simplifications and done some detective work already ;-)


> > Programm was running .After 1 hour it was still running but there was no
> > output.
> >
>
> If I calculate the number of hydrogen bonds as a function of time in
> water (no vacuum) using the same command line then there was  no problem.
>
>Same problem when I used g_rdf in vacuum.The commad line I have used
>g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also
> checked with -nopbc with the same command line.
>


RDF of what, in vacuum? What groups did you use?


>The programm is running but in the output file nothing is written.
>If I used g_rdf in water using the same command line there was no
> problem.
>

OK - but does your analysis make sense in vacuum?

Mark

Thanks Mark for your reply


In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I
want to calculate the distance between O atom and N-H hydrogen atom using
g_rdf in vacuum.


Similarly using the same index file I want to calculate the number of
hydrogen bonds as a function of time in vacuum using g_hbond.
Yes there is a H bond between C=O oxygen atom of i-th residue and N-H
hydrogen of i+4-th residue.
 I also checked with shorter trajectory there is also same problem .

Please let me know If there are any mistakes.

-
santu
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