Re: [gmx-users] DNA orientation restrain

[lina]

On Monday 01,October,2012 01:44 PM, 仝督读 wrote:
> Hi everyone,
> 
> I am doing a DNA simulation in a long simulation box (the lengthen of z is
> much larger than x and y). So I want to constrain the DNA molecule lying
> along the z axis. But I don't know how to realize this in GROMACS.
> 
> Actually I notice there is orientation restraints in 4.3.5 of GMX Manual.
> But the orientation value is set to be observables of NMR experiments, such
> as this example:
> ; ai aj type exp. label alpha const. obs. weight
> 31 32 1  1  3  3  6.083  -6.73  1.0
> But how can I set the observable in my case as it's not an NMR experiment?
> 
> Any suggestion will be appreciate.
> Thanks very much

Dudu,

notice the posre.itp?

; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 5 1  1000  1000  1000


change the fz value to be high enough, like below:

1 1  1000  1000  5

this 5 I just made up here as example, you may try to pick a
reasonable one.
> 
> Dudu Tong
> <31%2032%201%201%203%203>

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Re: [gmx-users] g_tcaf segmentation fault

[lina]

On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote:
> Thanks for the suggestion.
> I just tried and the problem presists. 
> Just to be clear, the right way is to use the g_covar.trr file, correct? 

 -f   traj.trr  InputFull precision trajectory: trr trj cpt

Here the full precision means double precision? I see you use single
precision.

I have never tried this one, perhaps someone else may give you some
suggestions.

Best regards,

> 
> Ο χρήστης lina  έγραψε:
> 
> On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
>> The -dt flag is the time step between the frames in ps. I tried the command 
>> in any combination i could think of. With -dt without, with -b without, and 
>> so on. The only way i get a partial result is to use the .trr file from the 
>> simulation and not from the g_covar command and even then i get the density 
>> of the system and after that "segmentation fault"
>>
> 
> Segmentation fault involves lots.
> If I were you, I would try -dt 100 or large to reduce memory
> requirement. or perhaps try the very short time period. namely -e 200 to
> see what's going on.
> 
>> Ο χρήστης lina  έγραψε:
>>
>> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
>>> Dear all,
>>>
>>> I am attempting to calculate the viscosity of a liquid binary system of
>>> 500 molecules (3050 atoms), via g_tcaf command.
>>> The system is equilibrated. The list of command I use is:
>>>
>>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
>>> eigenvec.trr -av average.pdb -l covar.log//
>>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
>>> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
>>> tcaf_fit.xvg/
>>
>> -dt 0.001 ?
>>
>>>
>>> The result is a Segmentation fault error:
>>>
>>> /Selected 0: 'System'//
>>> //trn version: GMX_trn_file (single precision)//
>>> //Last frame -1 time0.000/*/
>>> /**/Segmentation fault/*
>>>
>>> I use GROMACS 4.5.5
>>>
>>> What am I doing wrong?
>>>
>>> Thanks in advance
>>> Stelios
>>>
>>
> 

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Re: [gmx-users] g_tcaf segmentation fault

[lina]

On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
> The -dt flag is the time step between the frames in ps. I tried the command 
> in any combination i could think of. With -dt without, with -b without, and 
> so on. The only way i get a partial result is to use the .trr file from the 
> simulation and not from the g_covar command and even then i get the density 
> of the system and after that "segmentation fault"
> 

Segmentation fault involves lots.
If I were you, I would try -dt 100 or large to reduce memory
requirement. or perhaps try the very short time period. namely -e 200 to
see what's going on.

> Ο χρήστης lina  έγραψε:
> 
> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
>> Dear all,
>>
>> I am attempting to calculate the viscosity of a liquid binary system of
>> 500 molecules (3050 atoms), via g_tcaf command.
>> The system is equilibrated. The list of command I use is:
>>
>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
>> eigenvec.trr -av average.pdb -l covar.log//
>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
>> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
>> tcaf_fit.xvg/
> 
> -dt 0.001 ?
> 
>>
>> The result is a Segmentation fault error:
>>
>> /Selected 0: 'System'//
>> //trn version: GMX_trn_file (single precision)//
>> //Last frame -1 time0.000/*/
>> /**/Segmentation fault/*
>>
>> I use GROMACS 4.5.5
>>
>> What am I doing wrong?
>>
>> Thanks in advance
>> Stelios
>>
> 

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Re: [gmx-users] g_tcaf segmentation fault

[lina]

On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
> Dear all,
> 
> I am attempting to calculate the viscosity of a liquid binary system of
> 500 molecules (3050 atoms), via g_tcaf command.
> The system is equilibrated. The list of command I use is:
> 
> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v
> eigenvec.trr -av average.pdb -l covar.log//
> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n
> index.ndx -mol -oc tcaf_cub.xvg  -oa tcaf_all.xvg -o tcaf.xvg -of
> tcaf_fit.xvg/

-dt 0.001 ?

> 
> The result is a Segmentation fault error:
> 
> /Selected 0: 'System'//
> //trn version: GMX_trn_file (single precision)//
> //Last frame -1 time0.000/*/
> /**/Segmentation fault/*
> 
> I use GROMACS 4.5.5
> 
> What am I doing wrong?
> 
> Thanks in advance
> Stelios
> 

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Re: [gmx-users] Protein ligand molecular dynamics simulation

[lina]

On Mon, Apr 16, 2012 at 11:01 PM, sai nitin  wrote:
> Hi all,
>
> I have done complex (protein + ligand) complex from autodock software using
> this complex im trying to follow
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
> tutorial
>
> But when i take complex structure directly from autodock result and run
> PDB2GMX it will give error because it is not recognizing ligand topology
> which is in complex structure.
> Then i followed justin tutorial took protein alone and applied Charmm27
> Force field and used generate ligand topologies using Swissparam tool
> (http://swissparam.ch/) when i do Editconf and created cubic box ligand is
> going away from protein.
>
> Actually my main task to place ligand in paraticular binding site in my
> protein and perform molecular dynamics.
>
> Can any body tell me how to do this..?

1] pdb2gmx generate ligands.top (if possible, basically you need
generate your ligand.itp by other ways) and rename it as ligands.itp
2] pdb2gmx generate protein.top and rename it as protein.itp (also
need delete some entry)
3] create the topol.top includes the ligands.itp and protein.itp, take
care the double entry.
(To make it easy, you may take some pdb with several chains. use
pdb2gmx and see how those top files combined together.)
4] The docked structure skip the pdb2gmx step. go directly to the editconf.

You may do a try, but it will be helpful if you are a bit familiar
with how to combine those top_files.

>
>
> Thanks in advance
>
> --
>
> Sainitin D
>
>
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Re: [gmx-users] the different protonation state of HIS

[lina]

On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett  wrote:
> Dear All,
>
> For the different protonation state of HIS, what are there 3-letter code for
> GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me
> to read? Do we still have any other confusing amino acids?

In pdb2gmx -his

you will get something like below

0. H on ND1 only (HSD)
1. H on NE2 only (HSE)
2. H on ND1 and NE2 (HSP)
3. Coupled to Heme (HIS1)

Then based on the pka value and the PH, you can make a choice.

>
> I am looking forward to getting a reply from you.
>
> Cheers,
>
> Acoot
>
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Re: [gmx-users] how to change the timestamp of a xtc file

[lina]

On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham  wrote:
>
>
> On 05/04/12, lina  wrote:
>
> On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai  wrote:
>> trjcat -settime or trjconv -t0
>
> Thank you, a further question, a trjcat-ed  xtc file, which timestamp like
>
> 0-5 0-2 0-5 0-3 ...
>
> Are there someway to update them all in the trjcated ones?
>
>
> I've no idea what you mean, but trjconv -settime is still your friend.

sorry I didn't say it clearly.

Well, I mean several xtc files
all starts with 0
but ends with 1 ns, 2 ns, 1 ns

I use trjcat -cat combine them together. now I wonder can make the
time continuously.

from 0 to 4ns.

Thanks,


>
> Mark
>
>
>
>
> Thanks ahead,
>
>>
>> On 2012-04-05 03:59:44PM +0800, lina wrote:
>>> Hi,
>>>
>>> A quick question, how can I change the .xtc file which beginning at 0,
>>> end at 1 ns to beginning at 5ns and end at 6ns.
>>>
>>> Thanks for any suggestions,
>>>
>>> Best regards,
>>> --
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>>
>> --
>> ==
>> Peter C. Lai                    | University of Alabama-Birmingham
>> Programmer/Analyst              | KAUL 752A
>> Genetics, Div. of Research      | 705 South 20th Street
>> p...@uab.edu                     | Birmingham AL 35294-4461
>> (205) 690-0808                  |
>> ==
>>
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[gmx-users] something about tpr file

[lina]

Hi,

suppose I lost original .tpr file,

can I get tpr file from the .xtc file ? I mean from the .xtc or trr
file, not by re-run grompp to generate tpr file.

Thanks ahead,

Best regards,
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Re: [gmx-users] which xtc file should be used for the trjconv command

[lina]

On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett  wrote:
> Dear All,
>
> In the on-line tutorial on lysozyme
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html),
> there is a command
>
> trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
>
> Will you please consider in that command whether we can change md_1_1.xtc to
> state.xtc?

Yes.

>
> I am looking forward to getting your reply.
>
> Cheers,
>
> Acoot
>
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Re: [gmx-users] how to change the timestamp of a xtc file

[lina]

On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai  wrote:
> trjcat -settime or trjconv -t0

Thank you, a further question, a trjcat-ed  xtc file, which timestamp like

0-5 0-2 0-5 0-3 ...

Are there someway to update them all in the trjcated ones?

Thanks ahead,

>
> On 2012-04-05 03:59:44PM +0800, lina wrote:
>> Hi,
>>
>> A quick question, how can I change the .xtc file which beginning at 0,
>> end at 1 ns to beginning at 5ns and end at 6ns.
>>
>> Thanks for any suggestions,
>>
>> Best regards,
>> --
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>
> --
> ==
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> p...@uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                  |
> ==
>
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[gmx-users] how to change the timestamp of a xtc file

[lina]

Hi,

A quick question, how can I change the .xtc file which beginning at 0,
end at 1 ns to beginning at 5ns and end at 6ns.

Thanks for any suggestions,

Best regards,
-- 
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Re: [gmx-users] em fatal error!

[lina]

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila  wrote:
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>     Getting the Right Output Means no Artefacts in Calculating Stuff
>
>     :-)  VERSION 4.0.5  (-:
>
>
>   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2008, The GROMACS development team,
>     check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
>     :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -f  minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  Input    Structure file: gro g96 pdb tpr tpb
> tpa
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n  index.ndx  Input, Opt.  Index file
>   -p  topol.top  Input    Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o em.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file: edr ene
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -nice    int    0   Set the nicelevel
> -[no]v   bool   yes Be loud and noisy
> -time    real   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
>     sites
> -maxwarn int    0   Number of allowed warnings during input
> processing
> -[no]zero    bool   no  Set parameters for bonded interactions without
>     defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
>     atomtypes
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program grompp, VERSION 4.0.5

You use Version 4.0.5.

If I remember correctly, the earlier version has different pname.
(seems one is NA+, one is NA)

If I were you, I would update to latest version and try.

> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do
>
>
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Re: [gmx-users] continue replica exchange MD

[lina]

On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas  wrote:
> Hello,
>
> Upon continuing a replica exchange MD simulation using the command
>
> mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1 
> -cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g logRemd_20ns.log -v -e 
> edrRemd_20ns.edr -stepout 2000

>From my side, I have no problem resuming or extending the REMD
simulations in V.4.5.5 and 4.5.4

Here is the command:

mdrun_g_f -s md_.tpr -multi 32 -replex 500  -cpi state_.cpt -append

    I use state_.cpt, not state.cpt

>
> I get the following output:
> **
> ...
> ...
> 500 steps,  1.0 ps (continuing from step 49430,     98.9 ps).
> 500 steps,  1.0 ps (continuing from step 49430,     98.9 ps).
>
> step 49430, will finish Wed Sep 12 16:09:33 2012
> step 5, will finish Thu May 24 11:23:04 2012
> Step 47546: resetting all time and cycle counters
>
> =>> PBS: job killed: walltime 604823 exceeded limit 604800
> Terminated
> **
>
> Apparently, the job runs for one week on a computer cluster (that is the 
> maximum time allowed), but it does not progress very much beyond step 49430.
>
> Also the log-file does not show any more steps:
> 
>           Step           Time         Lambda
>          46455       92.91000        0.0
>
> Grid: 18 x 17 x 25 cells
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.83095e+04    3.70277e+04    2.14102e+03    8.83853e+03   -7.33070e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29503e+05    3.04138e+05   -2.66781e+04   -8.51221e+03   -2.74692e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59421e+05    5.41532e+03   -3.09689e+06    5.18959e+05   -2.57793e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97550e+02   -1.14933e+02    5.41944e+01    0.0e+00
>
> Writing checkpoint, step 49430 at Fri Jan 27 09:43:23 2012
>
> ---
> Restarting from checkpoint, appending to previous log file.
> ...
> ...
> Started mdrun on node 0 Tue Mar  6 16:40:10 2012
>
>           Step           Time         Lambda
>          49430       98.86000        0.0
>
> Grid: 18 x 17 x 25 cells
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.84241e+04    3.69121e+04    2.09533e+03    8.80916e+03   -4.67086e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29528e+05    2.99825e+05   -2.67028e+04   -8.51334e+03   -2.74410e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59506e+05    5.47116e+03   -3.09823e+06    5.18993e+05   -2.57923e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97570e+02   -1.14963e+02    2.67842e+00    0.0e+00
>
>           Step           Time         Lambda
>          5      100.0        0.0
>
>   Energies (kJ/mol)
>       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>    5.86161e+04    3.71585e+04    2.15336e+03    8.92946e+03   -4.84684e+02
>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>    2.29950e+05    3.01014e+05   -2.66724e+04   -8.51306e+03   -2.74349e+06
>   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
>   -9.59537e+05    5.56712e+03   -3.09531e+06    5.19371e+05   -2.57594e+06
>    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>    2.97787e+02   -1.14956e+02    2.36460e+01    1.50068e-05
> [End of log-file]
> ***
>
> I wonder, if this is my mistake (using the mdrun wrongly), a Gromacs problem 
> or maybe a problem of the computer cluster (MPI, etc). I would be grateful 
> for any help.
>
> Many thanks
> Andreas--
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Re: [gmx-users] Generating topology

[lina]

On Thu, Mar 22, 2012 at 11:54 AM, Spring buds  wrote:
> Hi
>
> A protein sits on the top of another protein (not docking). I then used
> pdb2gmx command to generate the topology. Surprisingly, i got  five files,
> as given below: I think the two proteins are not connected each other. is it
> possible to make it one posre and topol file.

You have already have one posre and topol.top

more topol.top
check what's inside your topol.top. pay attention to "include"
>
> Many thanks in advance
>
> posre_Protein_chain_A.itp
> posre_Protein_chain_A2.itp
> topol.top
> topol_Protein_chain_A.itp
> topol_Protein_chain_A2.itp
>
>
>
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.

Might your distance -dist so large.

try a smaller one and see.
>
>
> Best regards
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> There is not any things related to list of atoms on the terminal.


t: 100  83 ILE 845 CG1  1.60274 (nm)
t: 100  83 ILE 846 CG2  1.63838 (nm)
t: 100  83 ILE 847 CD  1.59769 (nm)
t: 100  83 ILE 848 C  1.8202 (nm)
t: 100  83 ILE 849 O  1.86972 (nm)
t: 100  84 ALA 850 N  1.88309 (nm)
t: 100  84 ALA 851 H  1.85958 (nm)
t: 100  84 ALA 853 CB  1.99705 (nm)
Last frame 50 time  100.000

gcq#310: "Shoot them the atom now" (The Ramones)

g_dist_g -f try_1.xtc -s try_1.tpr -dt 5 -b 0 -e 100 -dist 2 -n index_1.ndx

>
>
> Best regards
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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian
 wrote:
> Dear Lina
>
> Thanks for your reply.
>
> Without the -dist 0.5, I get the -o dist.xvg output, but I need list
> of the all atoms in group 2 closer than dist to the center of mass of
> group 1.

It print on the terminal, you may notice it.

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Re: [gmx-users] g_dist without output file

[lina]

On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian
 wrote:
> Dear all
>
> When I use  g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5,
> program was done without error, but it don't create output file
> (dist.xvg) in the directory in which g_dist tool was run.
>
> What is reason of this case?

Try without the -dist 0.5, you will get the -o dist.xvg output.

the -dist is Print all atoms in group 2 closer than dist to
the center of mass of group 1


>
>
> Any help will highly appreciated.
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Re: [gmx-users] dssp and gromacs version

[lina]

On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham  wrote:
> On 2/03/2012 6:52 PM, lina wrote:
>>
>> Hi,
>>
>> is the old dssp not compatible with the gromacs 4.5.5 ?
>>
>> I am confused,
>>
>> Thanks,
>>
>> Best regards,
>
>
> The new DSSP is not compatible with any GROMACS

Ha ... the dssp complain the segmentation fault in 4.5.5, but can run
smoothly in 4.5.3.

IIRC, seems there were some threads talked about that before.

>
> Mark
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[gmx-users] dssp and gromacs version

[lina]

Hi,

is the old dssp not compatible with the gromacs 4.5.5 ?

I am confused,

Thanks,

Best regards,
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Re: [gmx-users] PBC - Protein and Ligands

[lina]

On 1 Mar, 2012, at 1:01, Steven Neumann  wrote:

> Dear Gmx Users,
>  
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The 
> problem I face is PBC which I cannot get rid of. I used:
>  
> 1.  First make your molecules whole if you want them whole (system).
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 2.  Cluster your molecules/particles if you want them clustered
>  
> 3.  Extract the first frame from the trajectory as reference for removing 
> jumps if you want to remove jumps.
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 4.  Remove jumps if you want to have them removed using the first frame 
> (system)
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
>  
> So the trajecory of my ligands is smooth but they do do bind to the different 
> periodic images. As i know it is impossible to obtain the proper trajectory 
> of all of them I just want to obtain the realistic final positions of my 
> system to extract pdb file for further umbrella sampling. Any suggestions?

You may wanna try 

Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 
1000

Please change dt if necessary. 


>  
> Steven
>  
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Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

[lina]

On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann  wrote:
> Thank you Vedat!
>
> Why do you use -DFLEXIBLE in md and in em?
> Why dont you use constraint algorithm (LINCS) in your simulation?

Otherwise, the system is easily explode with lots of LINCS warning.

Also thanks Vedat for sharing,

Best regards,

>
> Steven
>
> On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz  wrote:
>>
>>
>> hi steven,
>>
>> i've been simulating a 33 AA peptide for the past two days using implicent
>> solvent in order to achieve a proper folding.
>>
>> i haven't added counterions, however, the systems shows nice results
>> according to what i've expected. the mdrun command (for the extension) for
>> our hardware looks as follows:
>>
>> mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt -deffnm md 2>&1
>>
>> and here's the mdp file for the energy minimization:
>>
>> define              =  -DFLEXIBLE
>> constraints         =  none
>> integrator          =  steep
>> dt                  =  0.001    ; ps
>> nsteps              =  3
>> vdwtype             =  cut-off
>> coulombtype         =  cut-off
>> pbc                 =  no
>> nstlist             =  0
>> ns_type             =  simple
>> rlist               =  0       ; this means all-vs-all (no cut-off), which
>> gets expensive for bigger systems
>> rcoulomb            =  0
>> rvdw                =  0
>> comm-mode           =  angular
>> comm-grps           =  Protein
>> optimize_fft        =  yes
>> ;
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  5.0
>> emstep              =  0.01
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  Still ; HCT ; OBC
>> nstgbradii          =  1
>> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
>> radii. Currently must be equal to rlist
>> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit
>> solvent
>> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
>> models, currently not used
>> sa_algorithm        =  Ace-approximation
>> sa_surface_tension  = -1
>>
>>
>> and for the md run:
>>
>> define              =  -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
>> constraints         =  none
>> integrator          =  md
>> dt                  =  0.001   ; ps
>> nsteps              =  10 ; 10 ps = 100 ns
>> nstcomm             =  10
>> nstcalcenergy       =  10
>> nstxout             =  1000     ; frequency to write coordinates to output
>> trajectory
>> nstvout             =  0       ; frequency to write velocities to output
>> trajectory; the last velocities are always written
>> nstfout             =  0       ; frequency to write forces to output
>> trajectory
>> nstlog              =  1000         ; frequency to write energies to log
>> file
>> nstenergy           =  1000     ; frequency to write energies to edr file
>>
>> vdwtype             =  cut-off
>> coulombtype         =  cut-off
>>
>> pbc                 =  no
>>
>> nstlist             =  0
>> ns_type             =  simple
>> rlist               =  0       ; this means all-vs-all (no cut-off), which
>> gets expensive for bigger systems
>> rcoulomb            =  0
>> rvdw                =  0
>>
>> comm-mode           =  angular
>> comm-grps           =  system
>>
>> optimize_fft        =  yes
>>
>> ; V-rescale temperature coupling is on
>> Tcoupl              =  v-rescale
>> tau_t               =  0.1
>> tc_grps             =  system
>> ref_t               =  300
>> ; Pressure coupling is off
>> Pcoupl              =  no
>> ; Generate velocites is on
>> gen_vel             =  yes
>> gen_temp            =  300
>> gen_seed            =  -1
>>
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent    =  GBSA
>> gb_algorithm        =  Still ; HCT ; OBC
>> nstgbradii          =  1
>> rgbradii            =  0   ; [nm] Cut-off for the calculation of the Born
>> radii. Currently must be equal to rlist
>> gb_epsilon_solvent  =  80    ; Dielectric constant for the implicit
>> solvent
>> ; gb_saltconc       =  0     ; Salt concentration for implicit solvent
>> models, currently not used
>> sa_algorithm        =  Ace-approximation
>> sa_surface_tension  = -1
>>
>>
>> best regards,
>> vedat
>>
>>
>> Am 28.02.2012 11:59, schrieb Steven Neumann:
>>
>>> Dear Gmx Users,
>>> I am using Gromacs 4.5.4 and I would like to implement implicit solvent
>>> for folding of my protein. I read mailing list and it is still confusing for
>>> me.
>>> Is it proper to use counterions within the system? If not, how can I
>>> obtain netral system?
>>> Do we use cut off for vdw and coulombic interactions?
>>> What kind of integrator should be used with a timestep?
>>> I will appreciate an mdp file for protein folding! Thank you
>>> Steven
>>
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[gmx-users] how to extract the x y z

[lina]

Hi,

I don't know how to extract the position like the x y z with t or r with t.

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] Error energy minimization on protein with implicit water

[lina]

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar  wrote:
>
> Dear Gromacs users,
>
> I have a MD simulated protein and i take frame from this and remove water
> and add water implicit in the interface and want to do energy minimization
> but while doing the minimization i get errors. The steps followed are-
>
> pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
> grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr
>
> The minim.mdp file =
>
> ; Lines starting with ';' ARE COMMENTS
> ; Everything following ';' is also comment
>
> title        = Energy Minimization    ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp        = /lib/cpp    ; Preprocessor
>
> ; Define can be used to control processes
> define  = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emtol        = 1000.0    ; Stop minimization when the maximum force < 1.0
emtol = 1.0
> kJ/mol
> nsteps        = 5000        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 1        ; Write energies to disk every nstenergy steps
> energygrps    = System    ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> ns_type        = simple      ; Method to determine neighbor list (simple,
> grid)
> coulombtype    = cut-off      ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.0        ; long range electrostatic cut-off
> rvdw        = 1.0        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = no        ; Periodic Boundary Conditions (yes/no)
>
> I get a note as =
> System has non-zero total charge: -4.96e+00
>
> then i tried using genion step as=
>
> genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log
>
> then again the grompp step and mdrun .
> but while doing mdrun i get an error as=
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
>
> but here i have given nsteps as 5000 so why does it stop.
> --
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
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Re: [gmx-users] how to get the block averaged MSD curve ?

[lina]

On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim  wrote:
> Hi,
>
> I have a simulation result from 0 to 50ns after equilibration run.
> I want to divide this data set equally into 10blocks (10ns each) and get
> block averaged MSD curve (average of 10 blocks).

I would try some external software. excel.

>
> It seems that I mange to get block MSD data by using  g_msd -beginfit 0
> -endfit 10, g_msd -beginfit 10 -endfit 20,
> Then the output files are msd1.xvg, msd2.xvg,..,msd10.xvg (10 xvg files)
>
> My question is that how can I get averaged MSD from this outputs??
> It seems that g_analyze is appropriate to do this.
>
> g_analyze -n 10 -av ??
>
> Could anybody tell me how to get averaged MSD using g_analyze (each block
> data has different x values but same length) ?
>
> Another question is that
> what is the difference bwn g_msd and g_analyze -msd ??
> Is there any reference of posting to obtain this information ?
>
>
>
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Re: [gmx-users] Problem with simulation of Protein-DNA complex

[lina]

On Thu, Feb 9, 2012 at 8:44 PM,   wrote:
> Dear Gromacs users,
>
> I have been trying to simulate a Protein-DNA complex using gromacs, but each
> time I have been facing problems. I would like to point out that both the
> Protein and DNA have been modeled and after that docked in order to obtain a
> complex. Following are the parameters I am using:
>
> Force-Field: amber99sb-ildn
> water model: TIP3P
>
> 40 NA ions were added in order to neutralise the complex-solvent system.
> Gromacs doesn't show any error up until I proceed to do nvt equilibriation.

Before the NVT, you may do some energy minimization.


> Following is nvt.mdp:
>
> title           = PFV_DNA_NVT
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 100       ; 2 * 5 = 100 ps
> dt              = 0.001         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracyi
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cels
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
>
> It generates a tpr, but upon mpirun gives the following error:
>
> starting mdrun 'Protein in water'
> 100 steps,   1000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.027514, max 0.979682 (between atoms 3460 and 3461)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   3455   3457   65.2    0.1542   0.2535      0.1526
>   3455   3456   33.3    0.1093   0.1322      0.1090
>   3457   3459   72.7    0.1105   0.1739      0.1090
>   3457   3458   65.7    0.1105   0.1588      0.1090
>   3460   3469   78.6    0.1409   0.2693      0.1400
>   3460   3461   78.8    0.1409   0.2772      0.1400
>   3461   3463   75.1    0.1406   0.1489      0.1400
>   3463   3465   37.2    0.1403   0.1756      0.1400
>   3463   3464   40.7    0.1083   0.1408      0.1080
>   3465   3467   35.5    0.1403   0.1733      0.1400
>   3467   3469   74.0    0.1405   0.1373      0.1400
>   3467   3468   42.9    0.1083   0.1433      0.1080
> Wrote pdb files with previous and current coordinates
>
> Step 1, time 0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 364940.065742, max 11977066.00 (between atoms 3465 and 3466)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   3475   3495  110.8    0.1526 20544.7148      0.1522
>   3475   3477  111.6    0.1529 20544.4336      0.1526
>   3475   3476  108.1    0.1094 20543.1309      0.1090
>   3477   3480   62.8    0.1527   4.6441      0.1526
>   3477   3479   57.5    0.1091   4.5683      0.1090
>   3477   3478   93.6    0.1091   4.6160      0.1090
>   3495   3497  138.1    0.1336   4.9133      0.1335
>   3495   3496   69.6    0.1230   4.9085      0.1229
>   3497   3499   40.2    0.1449   0.2036      0.1449
>   3497   3498   43.8    0.1010   0.1527      0.1010
>   3480   3483   35.6    0.1526   0.1902      0.1526
>   3480   3482   42.2    0.1090   0.1501      0.1090
>   3480   3481   41.7    0.1090   0.1485      0.1090
>   3453   3455   88.7    0.1701 117322.3672      0.14

Re: [gmx-users] trjconv select group

[lina]

On Friday 03,February,2012 10:02 PM, francesca vitalini wrote:

Sure!
My code is

#!/bin/bash
for ((i=1; i<=357; i=$i+3))
do
trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
../cg_gro/300-${i}.gro -pbc whole



try touch a file as index.txt and put 0 in the index.txt

trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o 
../cg_gro/300-${i}.gro -pbc < index.txt



done

very stupidly I just need to type 0 all the time in the interactive
window that trjconv opens.
Any help?







Thanks

2012/2/3 lina mailto:lina.lastn...@gmail.com>>

On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:

Yes but those tips are not for bash scripts... :(


You'd better post what you have done so far about this script,

probably someone can help you improve or refine it.





2012/2/3 Mark Abraham mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>


On 4/02/2012 12:21 AM, francesca vitalini wrote:

Hi!
I have to use the gromacs command trjconv to obtain a
.gro file
from a .xtc and a .pdb file. I have to do it for several
files
in a bash for loop so I'd rather prefer to find a way to
make my
script type in the trjconv interactive terminal always
the same
number for the system. Any tips?


Check out

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

<http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts>


<http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts

<http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts>>

Mark

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Re: [gmx-users] trjconv select group

[lina]

On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:

Yes but those tips are not for bash scripts... :(


You'd better post what you have done so far about this script,

probably someone can help you improve or refine it.






2012/2/3 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 4/02/2012 12:21 AM, francesca vitalini wrote:

Hi!
I have to use the gromacs command trjconv to obtain a .gro file
from a .xtc and a .pdb file. I have to do it for several files
in a bash for loop so I'd rather prefer to find a way to make my
script type in the trjconv interactive terminal always the same
number for the system. Any tips?


Check out
http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts


Mark

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Re: [gmx-users] reg. error

[lina]

On Fri, Feb 3, 2012 at 12:54 PM, Vishwambhar Bhandare
 wrote:
> Hello,
> I am getting error given below,
> wht we can do for this?
>
>
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
> 655
>
> Fatal error:
> Atom 'H5T in residue A 1 was not found in rtp entry RA5 with 31 atoms
> while sorting atoms.

Pay attention to check the residue A 1 in your input .gro file, and
then check the .rtp file in the
some_path_to/share/gromacs/top/_your_choice_of_force_field/rtp file.
> .
>
> Thanks and Regards,
> --
> Vishwambhar
> Centre for Bioinformatics
> Pondicherry University
> Pondicherry
> --
>
>
>
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Re: [gmx-users] Minimization Problems

[lina]

On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling  wrote:
> Hello,
>
> I've recently been having trouble with my simulations blowing up.
> Specifically,
>
> "This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size"
>
> for a few interactions, with each of them approaching inf.
>
> Can anyone find anything glaringly wrong with my .mdp?
>
> Thanks,
> Alex Seling
>
> title = Minimization of alpha-synuclein
> cpp = /lib/cpp -traditional
> define = -DFLEXIBLE
> integrator = sd
> constraints = none
> tinit = 0
> dt = 0.001
> nsteps = 100
> emtol = 0.1
> emstep = 0.1
> nstcgsteep = 1000
> bd-fric = 0
> nstlog = 50
> nstenergy = 1
> gen_temp = 273
> gb_epsilon_solvent = 78.3
> implicit_solvent = GBSA
> gb_algorithm = Still
> nstcomm = 10
> xtc_precision = 1000
> gen_vel = yes
> nstxtcout = 0
> nstxout = 100
> pbc = no
> energygrps = system
> nstfout = 0
> nstvout = 0
> niter = 20
> nstlist = 10

it's more about your .gro file (system), less about the .mdp file.

>
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Re: [gmx-users] simulation killed

[lina]

On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> did you write this script yourself?
>>
>
> This script appears to be based on one that I provided in the free energy
> tutorial, but there are some differences (including one of the mistakes you

Your tutorials were well-written. I read some of them. but not this one. so ...

> note below).  It would be helpful if the OP explained what these simulations
> were doing, as well as if they are attempting the tutorial or some other
> different system.
>
> -Justin
>
>
>> On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik 
>> wrote:
>>>
>>> hi! lina my script this please tell me where is
>>> wrong...thanks
>>>
>>>
>>> #!/bin/bash
>>>
>>> # Set some environment variables
>>> FREE_ENERGY=/home/mkiytak/Free_Energy1
>>> echo "Free energy home directory set to $FREE_ENERGY"
>>>
>>> MDP=$FREE_ENERGY/MDP
>>> echo ".mdp files are stored in $MDP"
>>>
>>> LAMBDA=0
>>>
>>> # A new directory will be created for each value of lambda and
>>> # at each step in the workflow for maximum organization.
>>>
>> Here add:
>>
>> if [ -d "Lambda_$LAMBDA" ]; then
>>        rm -r Lambda_$LAMBDA
>> fi
>>
>>> mkdir Lambda_$LAMBDA
>>> cd Lambda_$LAMBDA
>>>
>>> #
>>> # ENERGY MINIMIZATION 1: STEEP  #
>>> #
>>> echo "Starting minimization for lambda = $LAMBDA..."
>>>
>>> mkdir EM_1
>>> cd EM_1
>>>
>>> # Iterative calls to grompp and mdrun to run the simulations
>>>
>>> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>>>
>>> mdrun -nt 8 -deffnm min$LAMBDA
>>>
>>>
>>> # 
>>> # ENERGY MINIMIZATION 2: L-BFGS #
>>> #
>>>
>>> cd ../
>>> mkdir EM_2
>>> cd EM_2
>>>
>>> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>>>
>>> # Run L-BFGS in serial (cannot be run in parallel)
>>>
>>> mdrun -nt 1 -deffnm min$LAMBDA
>>>
>>> echo "Minimization complete."
>>>
>>>
>>>
>>> #
>>> # NVT EQUILIBRATION #
>>> #
>>> echo "Starting constant volume equilibration..."
>>>
>>> cd ../
>>> mkdir NVT
>>> cd NVT
>>>
>>> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3
>>
>>
>> One thing, do you use  define         = -DPOSRES in your nvt_0.mdp, if
>> yes, you need take care where your posre.itp file stored.
>>
>>> mdrun -nt 8 -deffnm nvt$LAMBDA
>>>
>>> echo "Constant volume equilibration complete."
>>>
>>>
>>>
>>> #
>>> # NPT EQUILIBRATION #
>>> #
>>> echo "Starting constant pressure equilibration..."
>>>
>>> cd ../
>>> mkdir NPT
>>> cd NPT
>>>
>>> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p
>>
>>
>> Here "$ LAMBDA" --> "$LAMBDA", no space.
>>
>>> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
>>> -maxwarn 3
>>>
>>> mdrun -nt 8 -deffnm npt$LAMBDA
>>>
>>> echo "Constant pressure equilibration complete."
>>>
>>>
>>> #
>>> # PRODUCTION MD #
>>> #
>>> echo "Starting production MD simulation..."
>>>
>>> cd ../
>>> mkdir Production_MD
>>> cd Production_MD
>>>
>>> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
>>> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
>>> -maxwarn 3
>>>
>>>
>>> mdrun -nt 8 -deffnm md$LAMBDA
>>>
>>> echo "Production MD complete."
>>>
>>> # End
>>> echo "Ending. Job completed for lambda = $LAMBDA"
>>>
>>&

Re: [gmx-users] simulation killed

[lina]

did you write this script yourself?

On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik  wrote:
> hi! lina my script this please tell me where is wrong...thanks
>
>
> #!/bin/bash
>
> # Set some environment variables
> FREE_ENERGY=/home/mkiytak/Free_Energy1
> echo "Free energy home directory set to $FREE_ENERGY"
>
> MDP=$FREE_ENERGY/MDP
> echo ".mdp files are stored in $MDP"
>
> LAMBDA=0
>
> # A new directory will be created for each value of lambda and
> # at each step in the workflow for maximum organization.
>
Here add:

if [ -d "Lambda_$LAMBDA" ]; then
rm -r Lambda_$LAMBDA
fi

> mkdir Lambda_$LAMBDA
> cd Lambda_$LAMBDA
>
> #
> # ENERGY MINIMIZATION 1: STEEP  #
> #
> echo "Starting minimization for lambda = $LAMBDA..."
>
> mkdir EM_1
> cd EM_1
>
> # Iterative calls to grompp and mdrun to run the simulations
>
> grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/HIS1/solv.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> mdrun -nt 8 -deffnm min$LAMBDA
>
>
> # 
> # ENERGY MINIMIZATION 2: L-BFGS #
> #
>
> cd ../
> mkdir EM_2
> cd EM_2
>
> grompp -f $MDP/EM/em_l-bfgs_$LAMBDA.mdp -c ../EM_1/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o min$LAMBDA.tpr -maxwarn 3
>
> # Run L-BFGS in serial (cannot be run in parallel)
>
> mdrun -nt 1 -deffnm min$LAMBDA
>
> echo "Minimization complete."
>
>
>
> #
> # NVT EQUILIBRATION #
> #
> echo "Starting constant volume equilibration..."
>
> cd ../
> mkdir NVT
> cd NVT
>
> grompp -f $MDP/NVT/nvt_$LAMBDA.mdp -c ../EM_2/min$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -o nvt$LAMBDA.tpr -maxwarn 3

One thing, do you use  define = -DPOSRES in your nvt_0.mdp, if
yes, you need take care where your posre.itp file stored.

>
> mdrun -nt 8 -deffnm nvt$LAMBDA
>
> echo "Constant volume equilibration complete."
>
>
>
> #
> # NPT EQUILIBRATION #
> #
> echo "Starting constant pressure equilibration..."
>
> cd ../
> mkdir NPT
> cd NPT
>
> grompp -f $MDP/NPT/npt_$ LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p

Here "$ LAMBDA" --> "$LAMBDA", no space.

> $FREE_ENERGY/HIS1/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
> -maxwarn 3
>
> mdrun -nt 8 -deffnm npt$LAMBDA
>
> echo "Constant pressure equilibration complete."
>
>
> #
> # PRODUCTION MD #
> #
> echo "Starting production MD simulation..."
>
> cd ../
> mkdir Production_MD
> cd Production_MD
>
> grompp -f $MDP/Production_MD/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p
> $FREE_ENERGY/HIS1/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
> -maxwarn 3
>
>
> mdrun -nt 8 -deffnm md$LAMBDA
>
> echo "Production MD complete."
>
> # End
> echo "Ending. Job completed for lambda = $LAMBDA"
>
>> Date: Mon, 30 Jan 2012 13:54:18 +0800
>
>> Subject: Re: [gmx-users] simulation killed
>> From: lina.lastn...@gmail.com
>> To: gmx-users@gromacs.org
>
>>
>> On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik 
>> wrote:
>> > hi again capacity of my harddisk 600 GB ı try again ..the
>> > program
>> > gave me below message...
>> >
>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
>> > Starting 8 threads
>> >
>> > NOTE: The load imbalance in PME FFT and solve is 1211%.
>> >   For optimal PME load balancing
>> >   PME grid_x (1152) and grid_y (1152) should be divisible by
>> > #PME_nodes_x (8)
>> >   and PME grid_y (1152) and grid_z (1152) should be divisible by
>> > #PME_nodes_y (1)
>> >
>> >
>> > Making 1D domain decomposition 8 x 1 x 1
>> > starting mdrun 'Protein in water'
>>
>> > 250 steps,   5000.0 ps.
>> > ./job_0.sh: line 95: 15777 Killed   mdrun -nt 8 -deffnm
>>
>> What's inside your job_0.sh?
>>
>> something wrong your script.
>>
>> > md$LAMBDA
>> >
>> > Production MD complete.
>> > Ending. Job completed for lambda = 0
>> > mkiytak@babil:~/JOB1$
>> >
>> >
>> > How can I solve this problemthanks for your help.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>&

Re: [gmx-users] Trajectory

[lina]

On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann  wrote:
> Dear Gmx Users,
>
> I run the simulation of protein with 10 ligands (200 ns). In total I should
> have total of 4000 frames as I set up:
>
> nsteps = 1
>
> dt = 0.002
>
> nstxout = 25000
>
> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump

-dt 4000

now you will only have 51 frames. more info. check trjconv -h

>
> The trajectory which I read in VMD has 3008 frames and my ligands completely
> disappear after 8 frame (They are not in PBC windows which I checked in
> Graphics -> Graphical Representation -> Periodic)
>
> Can you please advise? I think I have to many frames in my trajectory, how
> can I reduce it in trjconv?
>
> Thank you,
>
>
>
> Steven
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] simulation killed

[lina]

On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik  wrote:
> hi again capacity of my harddisk 600 GB ı try again ..the program
> gave me below message...
>
> Reading file md0.tpr, VERSION 4.5.4 (single precision)
> Starting 8 threads
>
> NOTE: The load imbalance in PME FFT and solve is 1211%.
>   For optimal PME load balancing
>   PME grid_x (1152) and grid_y (1152) should be divisible by
> #PME_nodes_x (8)
>   and PME grid_y (1152) and grid_z (1152) should be divisible by
> #PME_nodes_y (1)
>
>
> Making 1D domain decomposition 8 x 1 x 1
> starting mdrun 'Protein in water'

> 250 steps,   5000.0 ps.
> ./job_0.sh: line 95: 15777 Killed  mdrun -nt 8 -deffnm

What's inside your job_0.sh?

something wrong your script.

> md$LAMBDA
>
> Production MD complete.
> Ending. Job completed for lambda = 0
> mkiytak@babil:~/JOB1$
>
>
> How can I solve this problemthanks for your help.
>
>
>
>
>
>
>
>> Date: Sun, 29 Jan 2012 10:43:53 -0600
>> From: p...@uab.edu
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] simulation killed
>
>>
>> something killed your job but it wasn't gromacs.
>> Your system has run time or memory requirements that your job exceeded.
>>
>> On 2012-01-29 06:40:29PM +0200, mehmet kıytak wrote:
>> > hi! all
>> >
>> > ı have to a big problem..ı am doing free energy calculation for a ligand
>> > (L
>> > histidine ) when ı perform mdrun .. my simulation stop ... the program
>> > gave
>> > me this message..
>> >
>> > Reading file md0.tpr, VERSION 4.5.4 (single precision)
>> > Starting 8 threads
>> > Making 1D domain decomposition 8 x 1 x 1
> & gt; > starting mdrun 'Protein in water'
>
>> > 250 steps, 5000.0 ps.
>> > ./job_0.sh: line 95: 15457 Killed mdrun -nt 8 -deffnm
>> > md$LAMBDA
>> > Production MD complete.
>> > Ending. Job completed for lambda = 0
>> > mkiytak@babil:~/JOB1$
>> >
>> >
>> > my mdp file..
>> >
>> > ; Run control
>> > integrator = sd ; Langevin dynamics
>> > tinit = 0
>> > dt = 0.002
>> > nsteps = 250 ; 5 ns
>> > nstcomm = 100
>> > ; Output control
>> > nstxout = 500
>> > nstvout = 500
>> > nstfout = 0
>> > nstlog = 500
>> > nstenergy = 500
>> > nstxtcout = 0
>> > xtc-precision = 1000
>> > ; Neighborsearching and short-range nonbonded interactions
>> > nstlist = 10
>> > ns_type = grid
>> > pbc = xyz
>> > rlist = 1.0
>> > ; Electrostatics
>> > coulombtype = PME
>> > rcoulomb = 1.0
>> > ; van der Waals
>> > vdw-type = switch
>> > rvdw-switch = 0.8
>> > rvdw = 0.9
>> > ; Apply long range dispersion corrections for Energy and Pressure
>> > DispCorr = EnerPres
>> > ; Spacing for the PME/PPPM FFT grid
>> > fourierspacing = 0.12
>> > ; EWALD/PME/PPPM parameters
>> > pme_order = 6
>> > ewald_rtol = 1e-06
>> > epsilon_surface = 0
>> > optimize_fft = no
>> &g t; ; Temperature coupling
>
>> > ; tcoupl is implicitly handled by the sd integrator
>> > tc_grps = system
>> > tau_t = 1.0
>> > ref_t = 300
>> > ; Pressure coupling is on for NPT
>> > Pcoupl = Parrinello-Rahman
>> > tau_p = 0.5
>> > compressibility = 4.5e-05
>> > ref_p = 1.0
>> > ; Free energy control stuff
>> > free_energy = yes
>> > init_lambda = 0.00
>> > delta_lambda = 0
>> > foreign_lambda = 0.05
>> > sc-alpha = 0.5
>> > sc-power = 1.0
>> > sc-sigma = 0.3
>> > couple-moltype = system
>> > couple-lambda0 = vdw ; only van der Waals interactions
>> > couple-lambda1 = non e ; turn off everything, in this case
>
>> > only vdW
>> > couple-intramol = no
>> > nstdhdl = 10
>> > ; Do not generate velocities
>> > gen_vel = no
>> > ; options for bonds
>> > constraints = h-bonds ; we only have C-H bonds here
>> > ; Type of constraint algorithm
>> > constraint-algorithm = lincs
>> > ; Constrain the starting configuration
>> > ; since we are continuing from NPT
>> > continuation = yes
>> > ; Highest order in the expansion of the constraint coupling matrix
>> > lincs-order = 12
>> >
>> > PLEASE HELP ME... WHY THE PROGRAM STOP ( KİLLED) SORRY FOR BAD ENGLİSH..
>>
>> > --
>> > gmx-users mailing list gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> --
>> ==
>> Peter C. Lai | University of Alabama-Birmingham
>> Programmer/Analyst | KAUL 752A
>> Genetics, Div. of Research | 705 South 20th Street
>> p...@uab.edu | Birmingham AL 35294-4461
>> (205) 690-0808 |
>> ==
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)s ubscribe requests to the list. Use

Re: [gmx-users] umbrella-drug

[lina]

On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi
 wrote:
> Dear gmx-users
> I am working on lipid membrane+drug system.I should do umbrella
> sampling in this procedure:
> 1.cat drug and lipid
> 2.energy minimization
> 3.run npt
> 4.run md_pull
> I want to pull drug into the membrane but gromacs pushes the drug to
> the sides of box.and this result is independent of drug location
> Also I have used 500 ps for my simulation time but when I use ngmx to
> see the process,it runs only 56 ps.why?
> What can I do when I want to move drug to the bilayer?
You may want to check the
pull_vec1
and
pull_k

> --
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[gmx-users] adding hydrogen

[lina]

Hi,

are there some tips of quick adding missing atoms ( namely hydrogens,
non-titrable ones, or some ligands ones) ?

Thanks,
-- 
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Re: [gmx-users] Installing & uninstalling of gromacs

[lina]

On Tue, Jan 24, 2012 at 11:42 AM, Spring buds  wrote:
> Hi lina,
>
> Thanks for reply. could you tell me how to remove completly the gromacs
> installation?

Which commands have you issued?

try make uninstall in the directory where you used make install
before. like Path_to//gromacs-4.5.5
and then make distclean
for a totally clear re-installation, removed the /gromac-4.5.5 and
re-untar the gromacs-4.5.5.tar.gz

before that, further check the lib and bin have totally removed or not.

Which OS you are working on?

>
>
> On Tue, Jan 24, 2012 at 2:31 AM, lina  wrote:
>>
>> On 24 Jan, 2012, at 1:53, Spring buds  wrote:
>>
>> > Dear Gromacs users,
>> >
>> > Greetings!!!
>> >
>> > I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for
>> > past four days. But still I am not able to. So I would like to ask some
>> > questions which are below.
>> >
>> >
>> > 1.My laptop is a dual core, which means two processors?.So should I need
>> > to install MPI?
>> >
>> --enable threads
>>
>> > 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used
>> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
>> > (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>> > However, I used "rm -rf /usr/local/gromacs" to remove installing I still 
>> > can
>> > see tha gromacs files with red background in "/usr/local/bin". Could you
>> > tell me I removed the gromacs installing?
>>
>> You have not.
>>
>> >
>> > 3.Could you please tell me the very simple steps for installatios, since
>> > I am a novice.
>>
>> http://www.gromacs.org/Downloads/Installation_Instructions
>>
>> >
>> > Many thanks in advance for your time and help.
>> >
>> > Huang Malai
>> > --
>> > gmx-users mailing list    gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
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Re: [gmx-users] Installing & uninstalling of gromacs

[lina]

On 24 Jan, 2012, at 1:53, Spring buds  wrote:

> Dear Gromacs users,
> 
> Greetings!!!
> 
> I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past 
> four days. But still I am not able to. So I would like to ask some questions 
> which are below.
> 
> 
> 1.My laptop is a dual core, which means two processors?.So should I need to 
> install MPI?
> 
--enable threads 

> 2.I installed gromacs 4.5.5 with mistakes. To remove installing, I used the 
> "which gromacs" and it shows as "/usr/bin/which: no mdrun in 
> (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>  However, I used "rm -rf /usr/local/gromacs" to remove installing I still can 
> see tha gromacs files with red background in "/usr/local/bin". Could you tell 
> me I removed the gromacs installing?

You have not.  

> 
> 3.Could you please tell me the very simple steps for installatios, since I am 
> a novice. 

http://www.gromacs.org/Downloads/Installation_Instructions

> 
> Many thanks in advance for your time and help.
> 
> Huang Malai
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Implicit solvent model in Gromacs

[lina]

On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
>>  wrote:
>>>
>>> Dear gromacs users list,
>>>
>>> I noticed that gromacs can perform simulations with an implicit solvent
>>> model using a GBSA method. Is it compatible with the CHARMM22 force
>>> field?
>>
>>
>> look for gbsa.itp showed
>>
>> amber03.ff/forcefield.itp
>> amber03.ff/gbsa.itp
>> amber94.ff/forcefield.itp
>> amber94.ff/gbsa.itp
>> amber96.ff/forcefield.itp
>> amber96.ff/gbsa.itp
>> amber99.ff/forcefield.itp
>> amber99.ff/gbsa.itp
>> amber99sb.ff/forcefield.itp
>> amber99sb.ff/gbsa.itp
>> amber99sb-ildn.ff/forcefield.itp
>> amber99sb-ildn.ff/gbsa.itp
>> amberGS.ff/forcefield.itp
>> amberGS.ff/gbsa.itp
>> oplsaa.ff/forcefield.itp
>> oplsaa.ff/gbsa.itp
>>
>> seems not.
>>
>
> It's called gb.itp in the charmm27.ff subdirectory.

Thanks. your information is very helpful. I know the answer asked on
another thread.

>
> -Justin
>
>
>>> Thanks,
>>>
>>>    Gianluca
>>>
>>> -
>>> Gianluca Interlandi, PhD gianl...@u.washington.edu
>>>                   +1 (206) 685 4435
>>>                   http://artemide.bioeng.washington.edu/
>>>
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
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>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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Re: [gmx-users] About g_rms and the XPM file format

[lina]

On Mon, Jan 23, 2012 at 9:56 PM, Víctor  wrote:
> Dear all,
>
> I've been trying to do a rmsd matrix of  two different trajectories by using
> g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> uses does something like this:
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     superimpose f1 , f2
>     calculateRMSD f1, f2
>
> Or like this (as I've seen in some other rmsd matrix calculation scripts):
>
> for each frame f in traj1:
>   superimpose f with first frame
>
> for each frame f1 in traj1:
>   for each frame f2 in traj2:
>     calculateRMSD f1, f2
>
> I've also been trying to convert the resulting xpm file to a readable file

BTW, xpm file is readable.
try:
more xpm or other tools your preferred to read.


> in order to process it using python. Is there any tool to do this kind of
> conversion?(Btw I've been trying to find this kind of tool with not much
> luck). There's enough info on the file to be able to parse it easily, but
> using a 3rd party tested tool would be more convenient.
>
> Thanks!
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC
>
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Re: [gmx-users] Implicit solvent model in Gromacs

[lina]

On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
 wrote:
> Dear gromacs users list,
>
> I noticed that gromacs can perform simulations with an implicit solvent
> model using a GBSA method. Is it compatible with the CHARMM22 force field?

look for gbsa.itp showed

amber03.ff/forcefield.itp
amber03.ff/gbsa.itp
amber94.ff/forcefield.itp
amber94.ff/gbsa.itp
amber96.ff/forcefield.itp
amber96.ff/gbsa.itp
amber99.ff/forcefield.itp
amber99.ff/gbsa.itp
amber99sb.ff/forcefield.itp
amber99sb.ff/gbsa.itp
amber99sb-ildn.ff/forcefield.itp
amber99sb-ildn.ff/gbsa.itp
amberGS.ff/forcefield.itp
amberGS.ff/gbsa.itp
oplsaa.ff/forcefield.itp
oplsaa.ff/gbsa.itp

seems not.

>
> Thanks,
>
>     Gianluca
>
> -
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>                    +1 (206) 685 4435
>                    http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -
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[gmx-users] force field

[lina]

Hi,

which gromacs force field shares the high "quasi-compatibility" with
the amber force field.

I checked the heme only exists in gromos and the charmn

while gbsa only shows in amber and oplsaa,

truth is that I don't know how to get the gbsa parameter for heme,

Thanks for any suggestions,

Best regards,
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Re: [gmx-users] Failed to lock: md.log. No locks available.

[lina]

On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li  wrote:
> There is a solution in this mailing list sometime before:
> mv md.log to some other folder and copy it back.
> Jianguo

I tried, not work.

Thanks,

> ____
> From: lina 
> To: Discussion list for GROMACS users 
> Sent: Friday, 13 January 2012, 18:51
> Subject: Re: [gmx-users] Failed to lock: md.log. No locks available.
>
> On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham 
> wrote:
>> On 13/01/2012 7:08 PM, lina wrote:
>>>
>>> Hi,
>>>
>>> Failed to lock: md.log. No locks available.
>>
>>
>> mdrun locks various files at various points. If it can't then GROMACS
>> won't
>> continue, but the problem lies with the file system, and not with GROMACS.
>> Possibly some phantom process still thinks it owns the file.
>
> It's something relevant to the server.
> I am not experienced to figure it out even did some rough try.
> will drop an email to administrator.
>
> Thanks,
>
>>
>> Mark
>>
>>
>>>
>>> still the same problem I met before,
>>>
>>> once I terminated, resume not work, there is a md.log file.
>>>
>>> $ mount
>>> /dev/sda1 on / type ext3 (rw)
>>> none on /proc type proc (rw)
>>> none on /sys type sysfs (rw)
>>> none on /dev/pts type devpts (rw,gid=5,mode=620)
>>> usbfs on /proc/bus/usb type usbfs (rw)
>>> none on /dev/shm type tmpfs (rw)
>>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>>> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
>>> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)
>>>
>>> The /home is mounting on the last one.
>>>
>>> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
>>> Memory: 114GB RAM
>>> HDD Size: 744GB
>>> OS: CentOS 4 (64-bits)
>>>
>>> Thanks for any suggestions,
>>>
>>> any additional info you need please let me know,
>>>
>>> Best regards,
>>
>>
>> --
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Re: [gmx-users] Failed to lock: md.log. No locks available.

[lina]

On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham  wrote:
> On 13/01/2012 7:08 PM, lina wrote:
>>
>> Hi,
>>
>> Failed to lock: md.log. No locks available.
>
>
> mdrun locks various files at various points. If it can't then GROMACS won't
> continue, but the problem lies with the file system, and not with GROMACS.
> Possibly some phantom process still thinks it owns the file.

It's something relevant to the server.
I am not experienced to figure it out even did some rough try.
will drop an email to administrator.

Thanks,

>
> Mark
>
>
>>
>> still the same problem I met before,
>>
>> once I terminated, resume not work, there is a md.log file.
>>
>> $ mount
>> /dev/sda1 on / type ext3 (rw)
>> none on /proc type proc (rw)
>> none on /sys type sysfs (rw)
>> none on /dev/pts type devpts (rw,gid=5,mode=620)
>> usbfs on /proc/bus/usb type usbfs (rw)
>> none on /dev/shm type tmpfs (rw)
>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
>> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)
>>
>> The /home is mounting on the last one.
>>
>> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
>> Memory: 114GB RAM
>> HDD Size: 744GB
>> OS: CentOS 4 (64-bits)
>>
>> Thanks for any suggestions,
>>
>> any additional info you need please let me know,
>>
>> Best regards,
>
>
> --
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[gmx-users] Failed to lock: md.log. No locks available.

[lina]

Hi,

Failed to lock: md.log. No locks available.

still the same problem I met before,

once I terminated, resume not work, there is a md.log file.

$ mount
/dev/sda1 on / type ext3 (rw)
none on /proc type proc (rw)
none on /sys type sysfs (rw)
none on /dev/pts type devpts (rw,gid=5,mode=620)
usbfs on /proc/bus/usb type usbfs (rw)
none on /dev/shm type tmpfs (rw)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs
(rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83)

The /home is mounting on the last one.

CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
Memory: 114GB RAM
HDD Size: 744GB
OS: CentOS 4 (64-bits)

Thanks for any suggestions,

any additional info you need please let me know,

Best regards,
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Re: [gmx-users] REMD error

[lina]

On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means system does 
not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat



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Re: [gmx-users] unscribe

[lina]

On Thursday 12,January,2012 09:36 AM, yp sun wrote:

Dear Sir,
I want to unscribe there emails, thank.


http://lists.gromacs.org/mailman/listinfo/gmx-users

at the bottom, fill in your email address and click Unsubscribe.




Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- *12年1月12日，周四, Mark Abraham //* 写道：


发件人: Mark Abraham 
主题: Re: [gmx-users] REMD error
收件人: "Discussion list for GROMACS users" 
日期: 2012年1月12日,周四,上午9:28

On 12/01/2012 11:54 AM, bharat gupta wrote:
 > Hi,
 >
 > I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
 >
 > mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
 > mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6:
cannot enable executable stack as shared object requires: Permission
denied
 >

You configured GROMACS to use shared libraries, but something about
them or your current environment doesn't work. Try rebuilding
GROMACS, building with static libraries, or discussing with your
system admins.

Mark
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[gmx-users] exploding system

[lina]

Hi,


I met a very untamed simulation system.

when I tried to run a short MD, it's collapsed with LINCS Warnings, It's 
under 317K


so I used energy minimizations after NVT, and run another NVT_2 again. 
(In vacuum, no NPT being applied here).


after that NVT_2, mainly increased the steps, run MD, it's collapsed 
again after 500ps,


so I used the energy minimization from that nvt_2.gro several times, and 
it's collapsed during energy minimizations.


Might I used wrong way of handling it. I tried 300K, which can run a bit 
further without collapse.


Thanks for any suggestions you may give.

Do I need to work hard on the energy minimization or?

Best regards,


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[gmx-users] which may caused this error

[lina]

Hi,

I have very high frequency meeting below error:

[hostname-c06:07555] *** Process received signal ***
[hostname-c06:07555] Signal: Segmentation fault (11)
[hostname-c06:07555] Signal code: Address not mapped (1)
[hostname-c06:07555] Failing at address: 0x2aaab3248120
[hostname-c06:07555] [ 0] /lib64/libpthread.so.0 [0x399440e7c0]
[hostname-c06:07555] [ 1]
/home/lina/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1cc1)
[0x2b7249a92d61]
[hostname-c06:07555] [ 2]
/home/lina/lib/libgmx_mpi.so.6(do_nonbonded+0xe8) [0x2b72499d99d8]
[hostname-c06:07555] [ 3]
/home/lina/lib/libmd_mpi.so.6(do_force_lowlevel+0x32f)
[0x2b724931c7bf]
[hostname-c06:07555] [ 4]
/home/lina/lib/libmd_mpi.so.6(do_force+0xbf5) [0x2b72493766c5]
[hostname-c06:07555] [ 5] mdrun_g_f(do_md+0x54ba) [0x41b1ca]
[hostname-c06:07555] [ 6] mdrun_g_f(mdrunner+0x1169) [0x415ae9]
[hostname-c06:07555] [ 7] mdrun_g_f(main+0x9c7) [0x41c027]
[hostname-c06:07555] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x3993c1d994]
[hostname-c06:07555] [ 9] mdrun_g_f(do_cg+0x191) [0x407e39]
[hostname-c06:07555] *** End of error message ***
--
mpirun noticed that process rank 52 with PID 7555 on node hostname-c06
exited on signal 11 (Segmentation fault).

I have made a clear installation with 4.5.5.

just please feel free to give some wild guess about what's the possible reasons,

Thanks with best regards,
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Re: [gmx-users] Implicit solvent tutorial

[lina]

On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul  wrote:
>
>
> lina wrote:
>>
>> On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
>>  wrote:
>>>
>>> Hi gmx_users,
>>> is there any tutorial for implicit solvent simulation available?
>>
>>
>> Hi,
>>
>> I tried it few days ago.
>>
>> 1] pdb2gmx the water model choose none.
>>
>> 2] after editconf, go to energy minimization directly
>> * It's important to relax the system well.
>>
>> 3] NVT
>>
>> 4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz
>> At bottom also attached the one I tried.
>>
>> If some part is wrong, please let me know.
>>
>
> You should not use PBC. Cutoffs should be infinite (i.e. all set to zero).
Thanks, I noticed the example in the gromacs-gpubench-dhfr.tar.gz use
PBC=no and Cut-off is infinite.

>  I have never achieved stable simulations with finite cutoffs, even long
> ones, in implicit solvent simulations.

Thanks for reminding.

>
> The tcoupl setting is ignored when using the sd integrator, and there is
> very little need to do any position restraining in implicit solvent
> simulations, as there is no solvent to relax, you're just restraining the
> protein and not accomplishing anything.  gen_vel should be set to "yes" to
> generate velocities following EM.

Thanks again, I restrained some peptides, another peptides are free.
hopefully it will work.

>
> -Justin
>
>
>> Thanks,
>>
>> define          = -DPOSRES
>> integrator      = sd
>> nsteps          = 10
>> dt              = 0.0005
>> nstxout         = 1000
>> nstvout         = 1000
>> nstxtcout       = 1000
>> nstenergy       = 1000
>> nstlog          = 1000
>> continuation    = yes
>> constraints     = all-bonds
>> ns_type         = grid
>> nstlist         = 1.0
>> rlist           = 1.0
>> rcoulomb        = 1.0
>> rvdw            = 1.0
>> coulombtype     = Cut-off
>> pme_order       = 4
>> fourierspacing  = 0.16
>> tcoupl          = V-rescale
>> tc-grps         = A B C
>> tau_t           = 0.1 0.1 0.1
>> ref_t           = 300 300 300
>> pbc             = xyz
>> gen_vel         = no
>> ld_seed         = -1
>> implicit_solvent = GBSA
>> gb_algorithm     = OBC
>> nstgbradii       = 1.0
>> rgbradii         = 1.0
>> gb_epsilon_solvent = 80
>> gb_dielectric_offset = 0.009
>> sa_algorithm         = Ace-approximation
>> sa_surface_tension   = 0.0054
>>
>>
>>> Thanks!
>>>
>>> --
>>> Gianluca Santoni,
>>> Institut de Biologie Structurale
>>> 41 rue Horowitz
>>> Grenoble
>>> _
>>> Please avoid sending me Word or PowerPoint attachments.
>>> See http://www.gnu.org/philosophy/no-word-attachments.html
>>>
>>> --
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>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] Implicit solvent tutorial

[lina]

On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
 wrote:
> Hi gmx_users,
> is there any tutorial for implicit solvent simulation available?

Hi,

I tried it few days ago.

1] pdb2gmx the water model choose none.

2] after editconf, go to energy minimization directly
* It's important to relax the system well.

3] NVT

4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz
At bottom also attached the one I tried.

If some part is wrong, please let me know.

Thanks,

define  = -DPOSRES  
integrator  = sd
nsteps  = 10
dt  = 0.0005
nstxout = 1000  
nstvout = 1000  
nstxtcout   = 1000  
nstenergy   = 1000  
nstlog  = 1000  
continuation= yes   
constraints = all-bonds 
ns_type = grid  
nstlist = 1.0   
rlist   = 1.0   
rcoulomb= 1.0   
rvdw= 1.0   
coulombtype = Cut-off   
pme_order   = 4 
fourierspacing  = 0.16  
tcoupl  = V-rescale 
tc-grps = A B C
tau_t   = 0.1 0.1 0.1   
ref_t   = 300 300 300   
pbc = xyz   
gen_vel = no
ld_seed = -1
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii   = 1.0
rgbradii = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension   = 0.0054


>
> Thanks!
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
> _
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
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Re: [gmx-users] Convert xpm to matrix

[lina]

On Sun, Dec 4, 2011 at 3:04 PM, Alex Jemulin  wrote:
> Dear all,
>
> I'd like to convert an xpm file to delimited CSV , because I need to import
> values in excel.
>
> Any suggestion?

Try to write some scripts to do this.

>
> Thanks
>
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Re: [gmx-users] how to understand this sentence

[lina]

Now I used mdrun -nt 2

it showed:

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.

and mdrun -nt 1 it showed:

Program mdrun, VERSION 4.5.4-dev-20110711-dadcb
Source code file:
/var/local/cache/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544

Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.


On Thu, Dec 1, 2011 at 11:38 AM, lina  wrote:
> On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham  wrote:
>> On 1/12/2011 3:25 AM, lina wrote:
>>>
>>> The Y-size of the box (1.999239) times the triclinic skew factor
>>> (1.00) is smaller than the number of DD cells (2) times the
>>> smallest allowed cell size (1.00)
>>>
>>> I don't understand the fatal error message it has been given during a
>>> simple run,
>>>
>>> I tested with large box already, during editconf I used -d 30 already,
>>>
>>> it's a very small peptide, the box dimension is   63.95000  60.76600
>>>  62.9990
>>
>> Your system may be too small to parallelize over the number of processors
>> you are using (and as usual, it would have been a good idea to supply your
>> mdrun command line unless you enjoy wasting time when people make wrong
>> guesses).
>
> As you can see it's a very small job, so I just run on laptop,
>
> now I changed the mdrun -nt 4
> it showed:
> Fatal error:
> The X-size of the box (3.994507) times the triclinic skew factor
> (1.00) is smaller than the number of DD cells (4) times the
> smallest allowed cell size (1.00)
>
>
> The Fatal error about the Y-size when I used mdrun -nt 8
>
> can you guess which is wrong here. on the last email the URL contains
> the md.mdp, topol.top and .gro files to run a mdrun.
>
> Thanks,
>
>>
>> Mark
>> --
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Re: [gmx-users] how to understand this sentence

[lina]

On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham  wrote:
> On 1/12/2011 3:25 AM, lina wrote:
>>
>> The Y-size of the box (1.999239) times the triclinic skew factor
>> (1.00) is smaller than the number of DD cells (2) times the
>> smallest allowed cell size (1.00)
>>
>> I don't understand the fatal error message it has been given during a
>> simple run,
>>
>> I tested with large box already, during editconf I used -d 30 already,
>>
>> it's a very small peptide, the box dimension is   63.95000  60.76600
>>  62.9990
>
> Your system may be too small to parallelize over the number of processors
> you are using (and as usual, it would have been a good idea to supply your
> mdrun command line unless you enjoy wasting time when people make wrong
> guesses).

As you can see it's a very small job, so I just run on laptop,

now I changed the mdrun -nt 4
it showed:
Fatal error:
The X-size of the box (3.994507) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (4) times the
smallest allowed cell size (1.00)


The Fatal error about the Y-size when I used mdrun -nt 8

can you guess which is wrong here. on the last email the URL contains
the md.mdp, topol.top and .gro files to run a mdrun.

Thanks,

>
> Mark
> --
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[gmx-users] Re: how to understand this sentence

[lina]

https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh

I uploaded the files here.

is it the box still small?

Thanks,

On Thu, Dec 1, 2011 at 12:25 AM, lina  wrote:
> The Y-size of the box (1.999239) times the triclinic skew factor
> (1.00) is smaller than the number of DD cells (2) times the
> smallest allowed cell size (1.00)
>
> I don't understand the fatal error message it has been given during a
> simple run,
>
> I tested with large box already, during editconf I used -d 30 already,
>
> it's a very small peptide, the box dimension is   63.95000  60.76600  62.99900
>
> Thanks
--
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[gmx-users] how to understand this sentence

[lina]

The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)

I don't understand the fatal error message it has been given during a
simple run,

I tested with large box already, during editconf I used -d 30 already,

it's a very small peptide, the box dimension is   63.95000  60.76600  62.99900

Thanks
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Re: [gmx-users] diffusion of the water at the micelle surface

[lina]

On Sat, Nov 26, 2011 at 11:17 PM,   wrote:
> When people do this for lipid bilayers, they compute depth-dependent
> diffusion profiles (often diffusion is computed separately for lateral
> diffusion and diffusion along the bilayer normal). Sounds like you might do
> something similar. I doubt that the standard gromacs tools will do this for
> you. If you don't hear from anybody about how to do this, then I'd suggest
> that you simply use g_dist to get the time-dependent distance for each water
> molecule and then use g_traj to output the coordinates of each water
> molecule and then script it yourself after reading one of the papers where
> people compute depth-dependent diffusion profiles for a lipid bilayer.
>
> Chris.
>
> -- original message --
>
> I would like to compute the translational diffusion around the micelle
> surface. I know that I can select the water molecules at x distance of the
> micelle surface with g_select (right ?) but how to use this file generated
> by g_select to compute de diffusion, since the index and/or the number of
> water will change with the simulation time .

You may try g_density, choose different time interval.

>
>
>
> Thank you for your response
>
>
>
> Stephane
>
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Re: [gmx-users] Adding ions using "genion"

[lina]

On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen  wrote:
> Dear,
> I create a box of water with 10 MIBC molecules on two opposite surfaces.
> then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to
> creat .tpr file before using the command "genion -s min.tpr -o add.gro
> -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this box.
> I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" again and
> appeared the warings :
> Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)
> Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)
> Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)

There is a mis-match between your .top file and .gro file.

> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 72]:
>   21754 non-matching atom names
>   atom names from topol.top will be used
>   atom names from add.gro will be ignored
> ..
> Fatal error:
> Too many warnings (2), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> then I tried with the command "grompp -f input_min.mdp -o min.tpr -c add.gro
> -maxwarn 2000" and it run well.
> However, when I kept working with the command "mdrun -s min -o min -c
> min.g96 -x min -e min -g min", the errors appeared as follow:
> Fatal error:
> 3 particles communicated to PME node 2 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Please help me to fix this problem.
> Many thanks.
>
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>
>
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Re: [gmx-users] No locks available.

[lina]

On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz  wrote:
> Hi,

Well, thanks, here comes the questions you asked before.

> what file system is this? What operating system on the compute node? In case
> it is a network file system what file system is used underneath and what
> operating system is the file server using? What version of GROMACS are you
> using?

CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
Memory: 114GB RAM
HDD Size: 744GB
OS: CentOS 4 (64-bits)

2.6.9-42.0.10.ELlargesmp #1 SMP Tue Feb 27 09:59:08 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

Gromacs, VERSION 4.5.3

If you need more information, please feel free to let me know.

Best regards,

> As you workaround you should be able to run with "mdrun -noappend".
> Roland
>
> On Sun, Nov 13, 2011 at 10:43 AM, lina  wrote:
>>
>> Hi,
>>
>> This is the first time I met:
>>
>> Fatal error:
>> Failed to lock: md.log. No locks available
>>
>> the disk is not saturated,
>>
>> md.log is normal,
>>
>> The job was stopped months ago, and now I planned to resume it with
>> all the necessary files kept intact.
>>
>> Thanks for pointing out which parts I should examine,
>>
>> Best regards,
>> --
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>>
>>
>>
>>
>
>
>
> --
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> 865-241-1537, ORNL PO BOX 2008 MS6309
>
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Re: [gmx-users] No locks available.

[lina]

On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz  wrote:
> Hi,
> what file system is this? What operating system on the compute node? In case
> it is a network file system what file system is used underneath and what
> operating system is the file server using? What version of GROMACS are you
> using?
> As you workaround you should be able to run with "mdrun -noappend".

Thanks,

There is no problem running a mdrun without appending.

Best regards,

> Roland
>
> On Sun, Nov 13, 2011 at 10:43 AM, lina  wrote:
>>
>> Hi,
>>
>> This is the first time I met:
>>
>> Fatal error:
>> Failed to lock: md.log. No locks available
>>
>> the disk is not saturated,
>>
>> md.log is normal,
>>
>> The job was stopped months ago, and now I planned to resume it with
>> all the necessary files kept intact.
>>
>> Thanks for pointing out which parts I should examine,
>>
>> Best regards,
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>
>
>
> --
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>
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[gmx-users] No locks available.

[lina]

Hi,

This is the first time I met:

Fatal error:
Failed to lock: md.log. No locks available

the disk is not saturated,

md.log is normal,

The job was stopped months ago, and now I planned to resume it with
all the necessary files kept intact.

Thanks for pointing out which parts I should examine,

Best regards,
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Re: [gmx-users] Topology dihedral or improper dihedral

[lina]

On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG  wrote:
> Hi there
>
> I am trying to build up a topology file for a tetra nitrogen molecule using
> Gromos UA and OPLS UA force field. Following are the molecules.
>
> 1. for     C
>   |
>  A.  C-C-C-C-C-C-C-N-C  and
>   |
>  C
>
>   C
>        |
>  B.   C-C-C-C-C-C-C-N-C-C-C-C-COOH
>    |
>   C
>
> I have several questions:
>
> For A, the first molecule, should I use improper dihedral for the N-(CH3)3
> or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any
> differences when using different force field (GROMOS and OPLS-UA)?
> For B, the second molecule, should I use improper dihedral for the N-(CH3)3
> or proer dihedral for C-C-N-C with multi 2? Is there any differences when
> using different force field (GROMOS UA and OPLS UA)?
>
> The first expression about improper didedral is a planer restriction. When
> read the manual it also refers to the tetrahedral structure like this tetra
> nitrogen functional group. My question is when it has
> really long hydrocarbon tail, I guess it will be hard to flip over to
> the mirror images. Or it is not true in the simulation?

You may take one built by other server, such as
http://davapc1.bioch.dundee.ac.uk/prodrg/

as reference, and built yourself if necessary.
>
> Thank you very much!!!
>
> Best!
> Xueming
>
>
>
>
>
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Re: [gmx-users] setting working directory

[lina]

On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod  wrote:
> Hi There!
>
>
>
> Is it possible to run mdrun from a shared directory and set the working
> directory to a local directory on the computer on which it runs, in order to
> decrease NFS load?

Yes. I attached a generic script, you can modify from it if you want.

##project set up by the user
GENERICNAME="Your_project_name"

## input data folder
INPUTDATAFOLDER=${HOME}/data


## cluster environment
 shared scratch folder
SCRATCH=${HOME}/globalscracth

 node local scratch folder
LOCALSCRATCH=${LOCALSCRATCH:-/scratch}/${USER}

## set up a unique tag suffix
JOBSUFFIX=$(date +%Y_%m_%d-%H_%M_%S-%N)-$$

## job name
JOBNAME=${GENERICNAME}-${JOBSUFFIX}


## share job working directory
JOBFOLDER=${SCRATCH}/${JOBNAME}
mkdir -p ${JOBFOLDER}

## local job working directory
LOCALJOBFOLDER=${LOCALSCRATCH}/${JOBNAME}
mkdir -p ${LOCALJOBFOLDER}

## let work on the local computer
cd ${LOCALJOBFOLDER}

## let transfert input data
cp -p ${INPUTDATAFOLDER}/*.data .

## let begin the job


## let transfert output data
mv outputdata.data ${JOBFOLDER}

## clean up the local scratch
cd ..
rm -rf ${JOBNAME}

## go home
cd

## exit
exit 0

##
## eos


>
>
>
> Thanks, Efrat
>
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Re: [gmx-users] problem with Threading during run

[lina]

On Mon, Oct 31, 2011 at 9:28 AM, Sanku M  wrote:
> Hi,
>  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
> make use of threading introduced in gromacs 4.5.x series, it does not work.
>  After issuing command like mdrun -v -s , I expected that for my 8-core
> processor which is not running any other jobs, the threading will show one
> job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using
> only 1 of the 8 processors. I was wondering whether there is any command

mdrun -t number_of_processors

> line I need to use to ensure the gromacs understands that there is 8
> processors in a core and force make full use of the entire machine.
> I have tried the same thing in another different cluster where I found that
> threading works with showing 800 % cpu usage . But, for this cluster , the
> threading does not work.
and make sure during your compile process, enable --threads

> Any help will be appreciated.
> Sanku
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Re: [gmx-users] lost ngmx

[lina]

On Sat, Oct 29, 2011 at 12:51 AM, Victor  wrote:
> Hello gmx-users
>
> I have  compiled gromacs on Debian/Linux wiht the option --with-x but the
> ngmx binary has not been generated. I don´t have gnome or kde installed, but
> I have installed xserver-xorg and I can export VMD with ssh.
> Do I need to install gnome or kde? if the answer is yes, Do I need to
> compile gromacs again? or Is there a way to just compile ngmx?

There is a .deb ball in the debian repository.

http://packages.debian.org/sid/gromacs

so you may try
sudo aptitude install gromacs

It will check the dependencies for you and install those dependent
package (which also contains the GNOME staff in it).

>
> Thanks in advance
>
> --
> Víctor E. Bahamonde Padilla
> Laboratorio Fisicoquimica Molecular
> Departamento de Química
> Facultad de Ciencias
> Universidad de Chile
> Phone: 562-978-7443
> vedua...@ug.uchile.cl
>
>
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Re: [gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar  wrote:
> Hi Lina,
>
> My previous reply was from before I looked at the graph. Have you
> considered that the molecule might be taking a stroll and turn back,
Ha ... stroll?!
> or goes to another side of the protein? Have you looked at the
> trajectory, in particular at the trajectory with the jumps removed?

I extracted the parts from 280ns to 300ns, the presentation of that
part protein is not whole.

In the former way, the time since 280ns till the end,  the small
molecular still outside the cell/box. even the minidist is very small
later.

I am not sure how to get the trajectory and view? (ngmx? )
>

Thanks,
> Cheers,
>
> Tsjerk
>
> On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar  wrote:
>> Hi Lina,
>>
>> Don't combine fitting, centering and pbc options. It may not work as
>> expected. That's why the workflow is given. Use separate passes. By the way,
>> first centering on the protein followed by putting molecules in the box
>> should also work.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Oct 28, 2011 9:01 AM, "lina"  wrote:
>>
>> On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar 
>> wrote: > Hi Lina, >
>>
>>> Try a _translational_ fit on the protein, follwed by a pass with -pbc
>>> nojump > > Hope it helps,
>>
>> Hi,
>>
>> Thanks.
>>
>> I tried trjconv_g -fit translation -pbc nojump, ideally it should work.
>>
>> but still not,
>>
>> after I tried the minidist, I noticed the peak around 270ns,
>>
>> I attached the figure, what's the possible reason for this distance?
>>
>> Thanks,
>>
>> P.S the box dimension   6.21279   6.21279   6.21279
>>
>>> > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" 
>>> > wrote: > > On Fri, Oct 28...
>>
>>> -- > gmx-users mailing list    gmx-users@gromacs.org >
>>> http://lists.gromacs.org/mailman/listinfo/g...
>>
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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Re: [gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar  wrote:
> Hi Lina,
>
> Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
>
> Hope it helps,

Hi,

Thanks.

I tried trjconv_g -fit translation -pbc nojump, ideally it should work.

but still not,

after I tried the minidist, I noticed the peak around 270ns,

I attached the figure, what's the possible reason for this distance?

Thanks,

P.S the box dimension   6.21279   6.21279   6.21279


>
> Tsjerk
>
> On Oct 28, 2011 6:27 AM, "lina"  wrote:
>
> On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar 
> wrote: > Hi Lina, > > Make su...
>
> I used the initial mdrun .tpr. After checking the generated pdb (total
> 51 frames), the first 28/29 frames both are together, but later are
> separated. (the intra_fit also not work as expected).
>
> So I think at beginning the reference initial ones are together.
>
> This .xtc were trjcat together, first 200ns and then extend to 500ns,
> the .pdb generated used dt 10ns.
>>
>> Cheers,
> Am I wrong in some places? Actually for other trajectories I had no
> problem (use the same way of handling it).
>
> Thanks,
>
>> > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" 
>> > wrote: > > Hi, > > I have ...
>
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Re: [gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar  wrote:
> Hi Lina,
>
> Make sure to use a reference in which the molecules are together (clustered)
> the way you want them.

I used the initial mdrun .tpr. After checking the generated pdb (total
51 frames), the first 28/29 frames both are together, but later are
separated. (the intra_fit also not work as expected).

So I think at beginning the reference initial ones are together.

This .xtc were trjcat together, first 200ns and then extend to 500ns,
the .pdb generated used dt 10ns.
>
> Cheers,
Am I wrong in some places? Actually for other trajectories I had no
problem (use the same way of handling it).

Thanks,
>
> Tsjerk
>
> On Oct 27, 2011 11:47 AM, "lina"  wrote:
>
> Hi,
>
> I have a problem using
>
> trjconv_g -pbc nojump
> or
>
> trjconv_g -pbc nojump -center
>
> I even tried the -pbc whole.
>
> The system is protein with a small molecular, for the first time
> period, when I checked on pymol.
> they are together, but later they apart, after show cell, protein
> inside the cell, while this small molecular outside,
>
> I did not meet such issue before, it's used  to be easy to fix the pbc
> problem, but not this one. a bit surprise,
>
> They are supposed to be together,
>
> Thanks for any advice,
> --
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Re: [gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham  wrote:
> On 28/10/2011 2:39 PM, lina wrote:
>>
>> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
>>   wrote:
>>>
>>> 
>>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>>> behalf of lina [lina.lastn...@gmail.com]
>>> Sent: Thursday, October 27, 2011 10:47 AM
>>> To: Discussion list for GROMACS users
>>> Subject: [gmx-users] trjconv and -pbc
>>>
>>> Hi,
>>>
>>> I have a problem using
>>>
>>> trjconv_g -pbc nojump
>>> or
>>>
>>> trjconv_g -pbc nojump -center
>>>
>>> I even tried the -pbc whole.
>>>
>>> The system is protein with a small molecular, for the first time
>>> period, when I checked on pymol.
>>> they are together, but later they apart, after show cell, protein
>>> inside the cell, while this small molecular outside,
>>>
>>> I did not meet such issue before, it's used  to be easy to fix the pbc
>>> problem, but not this one. a bit surprise,
>>>
>>> They are supposed to be together,
>>>
>>> Thanks for any advice,
>>>
>>>
>>>
>>> I am sure it will help. Follow the workflow!
>>>
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc
>>>
>>> Just use the trjconv -h to see each option.
>>
>> Ha, I think I have tried those options. That's why I am confused.
>>
>> Thanks,
>
> Well, you need to try them better :) If you want your trajectory to keep
> protein and something else together, you will need an index group that
> combines them not jumping, and then combines them centering (or whatever).

Thanks. I did use the index group on trjconv to output the pdb of the
protein and the small molecular.

>
> Mark
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Re: [gmx-users] trjconv and -pbc

[lina]

On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
 wrote:
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of lina [lina.lastn...@gmail.com]
> Sent: Thursday, October 27, 2011 10:47 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] trjconv and -pbc
>
> Hi,
>
> I have a problem using
>
> trjconv_g -pbc nojump
> or
>
> trjconv_g -pbc nojump -center
>
> I even tried the -pbc whole.
>
> The system is protein with a small molecular, for the first time
> period, when I checked on pymol.
> they are together, but later they apart, after show cell, protein
> inside the cell, while this small molecular outside,
>
> I did not meet such issue before, it's used  to be easy to fix the pbc
> problem, but not this one. a bit surprise,
>
> They are supposed to be together,
>
> Thanks for any advice,
>
>
>
> I am sure it will help. Follow the workflow!
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc
>
> Just use the trjconv -h to see each option.

Ha, I think I have tried those options. That's why I am confused.

Thanks,

>
> Jan
>
> ===
> Jan Marzinek
> PhD Candidate
> Centre for Process Systems Engineering
> Department of Chemical Engineering
> Imperial College London
> South Kensington Campus
> London SW7 2AZ
> E: j.marzine...@imperial.ac.uk
> M: +44(0)7411 640 552
>
>
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[gmx-users] trjconv and -pbc

[lina]

Hi,

I have a problem using

trjconv_g -pbc nojump
or

trjconv_g -pbc nojump -center

I even tried the -pbc whole.

The system is protein with a small molecular, for the first time
period, when I checked on pymol.
they are together, but later they apart, after show cell, protein
inside the cell, while this small molecular outside,

I did not meet such issue before, it's used  to be easy to fix the pbc
problem, but not this one. a bit surprise,

They are supposed to be together,

Thanks for any advice,
-- 
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Re: [gmx-users] Domain decomposition error in alchemical free energy perturbation MD

[lina]

On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He  wrote:
> Dear all,
> I'm doing an "slow-growth" alchemical free energy perturbation calculation
> of the formation of a disulfide bridge between two Cysteines with Gromacs.
> I've had tried different ways to combine the topology of both state A and
> state B, and finally settled with the most direct way -- to "mutate" the
> atoms that have different partial charges in the two states, and transform
> the two hydrogen atoms into "dummy" atoms. As suggested by Gromacs manual
> and some messages from the internet, I put explicitly the OPLS parameters
> for the bonds, pairs, angles and dihedrals changed from state A to state B,
> and the grompp didn't give a warning. But when I was testing the production
> simulation on two processors, there was a warning of fatal error in the log
> file:
> =
> Initializing Domain Decomposition on 2 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205
>   multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417
> Minimum cell size due to bonded interactions: 4.151 nm
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm
> The maximum allowed number of cells is: X 0 Y 0 Z 0
> ---
> Program mdrun, VERSION 4.5.4
> Source code file: domdec.c, line: 6436
> Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 5.18876 nm
> Change the number of nodes or mdrun option -rdd or -dds

as suggested by the log:

1] Change the number of nodes
or
2] mdrun option -rdd or -dds



> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> =
> The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12
> respectively. I checked the topology and found no entries containing both
> these atoms. What's weird is that there's no way for these two atoms to have
> bonded interactions, but it says in the log that they have a two-body bonded
> interaction with a distance of 3.774 nm, which I cannot understand.
> Does anyone have an explanation what this could mean? Any suggestion is
> appreciated!
> Thanks in advance!
>
> Xiaoxiao He
> Oct. 15, 2011
>
>
> Attached are the input  parameters for the production md:
> =
> -Input Parameters:
>    integrator           = sd
>    nsteps               = 200
>    init_step            = 0
>    ns_type              = Grid
>    nstlist              = 10
>    ndelta               = 2
>    nstcomm              = 10
>    comm_mode            = Linear
>    nstlog               = 100
>    nstxout              = 10
>    nstvout              = 10
>    nstfout              = 10
>    nstcalcenergy        = 10
>    nstenergy            = 100
>    nstxtcout            = 1000
>    init_t               = 0
>    delta_t              = 0.0005
>    xtcprec              = 1000
>    nkx                  = 36
>    nky                  = 36
>    nkz                  = 36
>    pme_order            = 4
>    ewald_rtol           = 1e-05
>    ewald_geometry       = 0
>    epsilon_surface      = 0
>    optimize_fft         = TRUE
>    ePBC                 = xyz
>    bPeriodicMols        = FALSE
>    bContinuation        = FALSE
>    bShakeSOR            = FALSE
>    etc                  = No
>    nsttcouple           = -1
>    epc                  = Berendsen
>    epctype              = Isotropic
>    nstpcouple           = 10
>    tau_p                = 1
>    ref_p (3x3):
>       ref_p[    0]={ 1.0e+00,  0.0e+00,  0.0e+00}
>       ref_p[    1]={ 0.0e+00,  1.0e+00,  0.0e+00}
>       ref_p[    2]={ 0.0e+00,  0.0e+00,  1.0e+00}
>    compress (3x3):
>       compress[    0]={ 4.5e-05,  0.0e+00,  0.0e+00}
>       compress[    1]={ 0.0e+00,  4.5e-05,  0.0e+00}
>       compress[    2]={ 0.0e+00,  0.0e+00,  4.5e-05}
>    refcoord_scaling     = No
>    posres_com (3):
>       posres_com[0]= 0.0e+00
>       posres_com[1]= 0.0e+00
>       posres_com[2]= 0.0e+00
>    posres_comB (3):
>       posres_comB[0]= 0.0e+00
>       posres_comB[1]= 0.0e+00
>       posres_comB[2]= 0.0e+00
>    andersen_seed        = 815131
>    rlist                = 1.3
>    rlistlong            = 1.3
>    rtpi                 = 0.05
>    coulombtype          = PM

Re: [gmx-users] Normal Mode Analysis

[lina]

On Sat, Oct 15, 2011 at 2:58 AM, James Starlight  wrote:
> Dear Gromacs users!
>
> I have couple of questions about some Gromacs features.
>
>
> 1- I'm looking for tutorial where I could find clear example of  force fied
> based Normal Mode Analysis via Gromacs
>
> E.g on first step I would like to prepare structure of my protein in
> pereodic boundary conditions and conduct energy minimization ( I've already
> can do it). Next I'd like to conduct full-atomic Normal Mode analysis and
> obtain motion trajectories along some lowest frequency modes for futher
> visualization in VMD. Finally I'd like to obtain information about
> frequencies ( eigenvalues) of each mode as well as frequencies of each
> residue fluctuations along different modes.
>
>
> 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via
> ussage of multi cores of my CPU. I've found possible sillution via MPI
> function but this way dowsnt work in my case. How I can activate
> hyperthreading function as well as other possible ways ?

If you installed from src, during configure
--enable-threads

if you installed via some package management tools, I guess they would
install this way by default.

try:

mdrun -t

>
>
> Thank you for your help
>
> James
>
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Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

[lina]

On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy  wrote:

> Hi All,
>
> I understand that there were already some discussions about new DSSP exec
> with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that
> this two DSSP and do_dssp do not compatible each other?
>
> I was running in Ubuntu 10.04, and this is what I got:
>
> do_dssp -f 300K.trr -s 300K.tpr -o dssp
>
> I choose 5 'Mainchain'
>
> Fatal error:
> Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ
> ddvDjL4J > /dev/null 2> /dev/null
>
>
> I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the
> latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work.
>
> Are there are any suggestion or correction in my step? Or what version of
> gromacs that work well with DSSP? Or should I get the older version of DSSP
> that work with do_dssp? And where can I find the older version of DSSP
> because I can't find the older version in:
> http://swift.cmbi.ru.nl/gv/dssp/ .
>

http://biskit.pasteur.fr/install/applications/dssp

You may click above link (untested, be careful).


> Thanx,
> Randy
>
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Re: [gmx-users] lipid membrane slicing

[lina]

On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan wrote:

> Hi,
>
> I have protein completely inserted into lipid membrane and would like to
> study order parameter around the protein as well as away from the protein.
>
> For this I would like to slice my membrane into parts.
>
> I tried the following command:
>
> g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2
>
> The output i get from this is as same as the one where i dont use -sl 2
> flag and it also doesnt show the different parts it has used for order
> parameter calculation.
>
> Please can I know how to slice my lipid membrane so that i can study order
> parameter for each part separately.
>

It seems that the lipid around the protein is not fixed, it's slowly flow
(fluid).

during some time interval, not exactly the same lipids around the protein.
maybe another different group.
so here -sl 2 won't serve well for what you wanna test.



>
>
> Kind Regards,
> chetan
>
>
> 
>
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
>
> 
>
> 
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Re: [gmx-users] Re: topology error

[lina]

On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA  wrote:

> only 59 particle variation found out of 230 ligand coordinates.
>
> On 8 October 2011 12:22, ITHAYARAJA  wrote:
>
>> Dear Sir,
>>
>>
>> I am actually simulating my protein with its ligand so I incorporated all
>> ligand (3) coordinates to my protein .gro file and placed its .itp file
>> also. I used gromas96 43a1 force field.
>>
>> I found following error when i was doing grompp for energy minimization. I
>> went through FAQ and checked all but i couldn't find what exactly it was.
>>
>> So, I attached that files to you. I need your help to solve this
>>
>> Program grompp, VERSION 4.5.1
>> Source code file: grompp.c, line: 377
>>
>> Fatal error:
>> number of coordinates in coordinate file (GR_b4ion.gro, 66074)
>>  does not match topology (GR.top, 66015)
>>
>
I used to count the atom numbers in .gro file and manually modify the
topology to make them match.


>
>>
>> --
>> **
>> Ithayaraja M,
>> Research Scholar,
>> Department of Bionformatics,
>> Bharathiar University,
>> Coimbatore 641 046,
>> Tamil Nadu
>> India
>>
>
>
>
> --
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
>
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[gmx-users] A quick Q: How to get the history in make_ndx

[lina]

Hi,

How do I use the history input in the make_ndx prompt,

such as before I input

name 32 A2
name 33 A3

up arrow showed me: > ^[[A
Alt+up arrow showed me: > ^[[1;3A

Just curious,

Thanks,
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Re: [gmx-users] snap shot

[lina]

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal wrote:

> Hello,
>
> I have a system with 128 emi (cations) and 128 Cl (anions). I run the
> simulation for 20 ns.
>
> I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.
>
trjconv  use -dt 5000

>
> I don't want to save snap shot for 128 ion-pairs. How can I take average
> over 128 ion pairs and save snap shot for a single ion pair.
>
I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b -e

you may wait for some other better answers.


> Basically I want to use classical md geometry for quatum chemical
> calculation.
>
> I am using Gromacs 4.0.7 version.
>
> Thanks
>
> Nilesh
>
>
>
>
>
>
>
>
>
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Re: [gmx-users] MD with membrane protein

[lina]

On Tue, Oct 4, 2011 at 2:57 AM, elisa carli  wrote:

> Hi Lisa
>
Thank you very much for your reply.
> After minimimization could I run a molecular dynamic production?
> Or have I to do other sets?
>
Yes, after energy minimization, you need do some other sets (like NVT and
NPT).

Could you write me which are the commands to execute up to MD run?
>

The links Justin provided are very useful. It's not a bad idea to do some
tutor to be familiar with those procedures.


>
> Bests
>
> 2011/9/22 lina 
>
>>  On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:
>>
>>> Dear All
>>>
>>> I'd like to perfom a MD simulation on a membrane protein using DLPC or
>>> DPPC system
>>> I've downloaded the API package from this link
>>> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>>>
>>> DPPC.zip and DLPC.zip by schiu
>>>
>>> How can I use them? Where can I get a tutorial or commands illustrating
>>> the use of these packages?
>>>
>>> Thanks in advance
>>>
>>  Here is a rough procedure:
>>
>> http://www.nanoconductor.org/43A1-S3/
>>
>> Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
>> the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
>> try it).
>>
>> pdb2gmx_g -f speptide.pdb -o speptide.gro
>>
>> choose
>> 9: GROMOS96 43a1 force field
>> 1: SPCsimple point charge, recommended
>>
>> $ tail -1 dppc.gro
>>5.68585   5.60685   6.85739
>>
>> To be as simple as possible here, we use the dimension of the dppc.gro
>>
>> editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2
>> -box  5.68585   5.60685   6.85739
>>
>> now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by
>>
>> genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top
>>
>>
>> Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,
>>
>> the purpose of doing a simple energy minimization here just want to "test"
>> the topol.top.
>>
>> it used 43A1-S3 force field (You can download from
>> http://www.nanoconductor.org/43A1-S3/).
>>
>> The head of topol.top:
>> ; Include forcefield parameters
>> #include "ffG43A1-S3.itp"
>> #include "lipids_43A1-S3.itp"
>>
>> The tail of topol.top:
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein 1
>> DPPC 71
>> SOL  3205
>>
>> I manually added DPPC  71.
>>
>> please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
>> ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
>> directory,
>> extra copy ff_dum.itp from
>> some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
>> directory.
>>
>> I attached all those files in try.tar.gz
>>
>> https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
>>
>> mdrun_g -v -deffnm em
>>
>> works well.
>>
>>
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>> --
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>
>
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-- 
Best Regards,

lina
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Re: [gmx-users] concentration distribution

[lina]

On Sep 25, 2011, at 0:33, raj  wrote:

> Hello,
> 
> I would like to calculate the concentration distribution of atoms along the x 
> and y axis from the trajectory. Can anybody suggest me a tool to calculate 
> this?

g_rdf ?!

> 
> regards,
> Raj
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Re: [gmx-users] diferent version of gcc

[lina]

2011/9/23 Víctor Bahamonde 

>  Hello gmx users
>
> I have a question related to gromacs compilation
> in the  same machine, are there any difference in the result of MD when I
> compile the same version of gromacs but with diferent version of gcc?
> also, gcc 4.1.x still broken?
> I use Debian 5 and Debian 6 on amd phenom II quad core.
>
>
http://packages.debian.org/sid/gromacs
http://packages.debian.org/wheezy/gromacs

They have had already well built .deb ball there.
Install from your favoriate package management.


Thanks in advance.
>
> *Víctor E. Bahamonde Padilla
> Laboratorio de Fisicoquímica Molecular
> Departamento de Química
> Facultad de Ciencias
> Universidad de Chile
> Phone: 562-978-7443
> vedua...@ug.uchile.cl*
>
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-- 
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lina
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Re: [gmx-users] error while install GMX4.5.5

[lina]

On Thu, Sep 22, 2011 at 8:11 PM, zhongjin  wrote:

> The system is Rocks 4.3 (Mars Hill), and
> [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc
> glibc-kernheaders-2.4-9.1.100.EL
> glibc-2.3.4-2.36
> glibc-headers-2.3.4-2.36
> glibc-common-2.3.4-2.36
> glibc-devel-2.3.4-2.36
>
> [hzj1000@ZhouGroup ~]$ gcc -v
> Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --enable-shared --enable-threads=posix
> --disable-checking --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-java-awt=gtk
> --host=i386-redhat-linux
> Thread model: posix
> gcc version 3.4.6 20060404 (Red Hat 3.4.6-8)
>
>
My gcc version is 4.6.1

probably it's nothing to do with your problem.

just probably you may wanna to undate your gcc.


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lina
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Re: [gmx-users] MD with membrane protein

[lina]

On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:

> Dear All
>
> I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC
> system
> I've downloaded the API package from this link
> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>
> DPPC.zip and DLPC.zip by schiu
>
> How can I use them? Where can I get a tutorial or commands illustrating the
> use of these packages?
>
> Thanks in advance
>
 Here is a rough procedure:

http://www.nanoconductor.org/43A1-S3/

Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide from
the gromacs tutorial (it's a bad choice to put it in the dppc, but we just
try it).

pdb2gmx_g -f speptide.pdb -o speptide.gro

choose
9: GROMOS96 43a1 force field
1: SPCsimple point charge, recommended

$ tail -1 dppc.gro
   5.68585   5.60685   6.85739

To be as simple as possible here, we use the dimension of the dppc.gro

editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2  -box
5.68585   5.60685   6.85739

now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by

genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top


Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,

the purpose of doing a simple energy minimization here just want to "test"
the topol.top.

it used 43A1-S3 force field (You can download from
http://www.nanoconductor.org/43A1-S3/).

The head of topol.top:
; Include forcefield parameters
#include "ffG43A1-S3.itp"
#include "lipids_43A1-S3.itp"

The tail of topol.top:

[ molecules ]
; Compound#mols
Protein 1
DPPC 71
SOL  3205

I manually added DPPC  71.

please copy the  lipids_43A1-S3.itpffG43A1-S3.itp
ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current
directory,
extra copy ff_dum.itp from
some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working
directory.

I attached all those files in try.tar.gz
https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB

mdrun_g -v -deffnm em

works well.


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Re: [gmx-users] Re: about non-writing issue

[lina]

On Mon, Sep 19, 2011 at 11:31 AM, Jianguo Li  wrote:

> I met the similar problem before, sometimes my job writes output, sometimes
> not. My cluster administrator fixed the problem and they told me that there 
> were
> some problem at some compute nodes which my job unfortunately was dispatched
> to.
>

Last time I contacted the administrator, he told me it's due to the
restriction he set, I mean, I could only use limited nodes.
He loosed the configuration a bit and it worked at that time.

But later it has happened, I don't have convincing confidence to email root
again.
So just try to figure out slowly.

Thanks for your answering,


>
> Jianguo
>
>
> --
> *From:* lina 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, 18 September 2011 5:13 PM
> *Subject:* [gmx-users] Re: about non-writing issue
>
> Hi,
>
> It works now.
>
> Not write (just based on guess) might
> the md.log step such as is 1114
> while use thread I noticed the actually run step started from 11135000
>
> so I run until it can write to the md.log
>
> then switch to 1 node to run for a while,
>
> then switch to more nodes.
>
> But there might be some reason there which I don't know.
>
> Thanks,
>
> On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:
>
> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>
>
>
> --
> Best Regards,
>
> lina
>
>
>
> --
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lina
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[gmx-users] Re: about non-writing issue

[lina]

Hi,

It works now.

Not write (just based on guess) might
the md.log step such as is 1114
while use thread I noticed the actually run step started from 11135000

so I run until it can write to the md.log

then switch to 1 node to run for a while,

then switch to more nodes.

But there might be some reason there which I don't know.

Thanks,

On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:

> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>


-- 
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lina
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[gmx-users] about non-writing issue

[lina]

Hi,

Very sporadically and also with high frequent,

The job I submitted only running without writing (this job is not un-started
one, mainly one I stopped and rerun).

Before I thought I did not wait long enough, such as hours, but seriously
after 3 or 8 hours, still running not writing.

I ssh to each nodes, all is fully running.

The storage is NFS, I/O flow can't be choked for hours.

Really headache, sometimes it works.

I have had no clue about it.


Thanks for any suggestions,


-- 
Best Regards,

lina
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Re: [gmx-users] How do I examine the results didn't write issue

[lina]

On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham wrote:

> On 12/09/2011 10:23 PM, lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>
> If you can run mdrun_threads -np 4 and get output and your mpirun -np 4
> mdrun_mpi does not write output, then there must be something wrong with
> your MPI environment. Try another MPI program and see what it does.
>

I guess I will drop an email to the administrator.

might be an MPI issue.

Thanks for your time,


> Mark
>
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lina
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Re: [gmx-users] How do I examine the results didn't write issue

[lina]

On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>> I am confused, why the job is running,
>>
>> but they did not write the .edr, .log .xtc ... files.
>>
>> Everything showed so normal, just not writing,
>>
>> when I used thread, all is fine, the writing is normal.
>>
>> just use mpi, I tried different nodes, still not work, now two hours
>> later, still no writing, just running.
>>
>> Thanks for providing any clue for me to examine.
>>
>>
>>
> Sounds like your MPI implementation is broken or you haven't issued the
> command right.  If you have a test command that you know should work, run
> that. Otherwise, it's impossible to know if the problem is with Gromacs or
> something external.  If you compiled with threading support, but not MPI (in
> a separate binary) then MPI will not work on the thread-enabled executable.
>

I suspected it's MPI issue, but couple of days ago it's fine, and the
results was able to write.

I installed both MPI and thread but with different prefix to distinguish.

Thanks,

>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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lina
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[gmx-users] How do I examine the results didn't write issue

[lina]

Hi,

I am confused, why the job is running,

but they did not write the .edr, .log .xtc ... files.

Everything showed so normal, just not writing,

when I used thread, all is fine, the writing is normal.

just use mpi, I tried different nodes, still not work, now two hours later,
still no writing, just running.

Thanks for providing any clue for me to examine.


-- 
Best Regards,

lina
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Re: [gmx-users] how to modify the md. log

[lina]

On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>> My job terminated due to the storage out of the quote given by
>> administrator,
>>
>> here the md.log is unusual, so when I resume the job, the results won't
>> append on it. but still running...
>>
>> Here is the tail of md.log,
>>
>>DD  step 31424999  load imb.: force 20.8%  pme
>> mesh/force 1.936
>>
>>   Step   Time Lambda
>>   31425000 62850.00.0
>>
>> <...snip...>
>>
>> DD  step 31425999  load imb.: force 23.7%  pme mesh/force
>> 1.923
>>
>>   Step   Time Lambda
>>   31426000 62852.00.0
>>
>>
>> <...snip...>
>>Kinetic En.   Total EnergyTemperature [lina@hostname
>>
>>
>> You may notice that the [lina@hostname] did not start in a new line.
>>
>> there is md_step31441735.cpt
>> and md_prev.cpt
>>
>> what is the final step stored in the md_prev.cpt? How do I check ?
>>
>>
> It should be the step -cpt minutes before the later checkpoint was written.
>  Use gmxcheck to verify its contents.
>
>
>  are there some chance to resume?
>>
>>
> Make sure the existing job has been killed (which sounds like it may or may
> not be the case) and simply restart from the appropriate checkpoint.
>
> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts<http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>
>
> -Justin
>

Thanks.


>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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lina
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Re: [gmx-users] radial distribution function

[lina]

On Sat, Sep 10, 2011 at 10:00 PM, Moeed  wrote:

> Thank you for your input. I am going to run for another 15 ns to see if the
> little jumps vanish.
>
> Best,
>
> g_rdf -bin
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[gmx-users] Re: how to modify the md. log

[lina]

On Sat, Sep 10, 2011 at 5:05 PM, lina  wrote:

> Hi,
>
> My job terminated due to the storage out of the quote given by
> administrator,
>
> here the md.log is unusual, so when I resume the job, the results won't
> append on it. but still running...
>
> Here is the tail of md.log,
>
> DD  step 31424999 load imb.: force 20.8%  pme mesh/force 1.936
>
>Step   Time Lambda
>3142500062850.00.0
>
> <...snip...>
>
> DD  step 31425999 load imb.: force 23.7%  pme mesh/force 1.923
>
>Step   Time Lambda
>3142600062852.00.00000
>
> <...snip...>
> Kinetic En.   Total EnergyTemperature [lina@hostname
>
>
> You may notice that the [lina@hostname] did not start in a new line.
>
> there is md_step31441735.cpt
> and md_prev.cpt
>
> what is the final step stored in the md_prev.cpt? How do I check ?
>

gmxcheck shows:

Last frame -1 time 62400.328

End of file on md.xtc but not on md_prev.cpt

Thanks,



>
>
>
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[gmx-users] how to modify the md. log

[lina]

Hi,

My job terminated due to the storage out of the quote given by
administrator,

here the md.log is unusual, so when I resume the job, the results won't
append on it. but still running...

Here is the tail of md.log,

DD  step 31424999 load imb.: force 20.8%  pme mesh/force 1.936

   Step   Time Lambda
   3142500062850.00.0

<...snip...>

DD  step 31425999 load imb.: force 23.7%  pme mesh/force 1.923

   Step   Time Lambda
   3142600062852.00.0

<...snip...>
Kinetic En.   Total EnergyTemperature [lina@hostname


You may notice that the [lina@hostname] did not start in a new line.

there is md_step31441735.cpt
and md_prev.cpt

what is the final step stored in the md_prev.cpt? How do I check ?

are there some chance to resume?

Thanks ahead,

Best regards,

lina
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Re: [gmx-users] radial distribution function

[lina]

On Sat, Sep 10, 2011 at 3:35 AM, Moeed  wrote:

> Dear users,
>
> I have created radial distribution function plot for Carbon atoms in a
> system containing polymer chains. I see some little jumps between first and
> second peak.
> I need your help to comment on how this behavior can be justified (or if
> the plot is wrong).
>
> g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
> Thank you in advance.
>

I think your figure is fine.

You just need how to proper interpret your figures, truly understand what
the "radial distribution" means.


>
>
>
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lina
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Re: [gmx-users] md.mdp file GPU one

[lina]

On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul  wrote:

>
>
> lina wrote:
>
>> Hi,
>>
>>
>> are there someone love to share one md.mdp file for GPU version?
>>
>>
> All the details are here:
>
> http://www.gromacs.org/**Downloads/Installation_**
> Instructions/GPUs?highlight=**gpu<http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu>
>
> The benchmark archive has example .mdp files that you can tweak.
>

Thanks. ( From those warnings, started to realize its limitations, no plan
to try further recently. ^_^ )


>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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lina
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[gmx-users] md.mdp file GPU one

[lina]

Hi,


are there someone love to share one md.mdp file for GPU version?


Thanks ahead,

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lina
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Re: [gmx-users] no output in g_dist

[lina]

On Thu, Sep 8, 2011 at 8:25 PM, aiswarya pawar  wrote:
> Hi users,
>
> To get the distance between water and protein i did -
>
>  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11
>
> from this i should obtain an output file as distance.xvg which i dont get.

The -dist option: Print all atoms in group 2 (water) closer than dist to
the center of mass of group 1 (protein in
your case).

As you have seen, it *print* the result on the screen.

To obtain the distance.xvg file, please don't use the -dist option here.

>
> and my output is printed on the terminal as-
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
> t: 1  136 SOL 2337 HW1  0.706358 (nm)
> t: 1  136 SOL 2338 HW2  0.807787 (nm)
> t: 1  139 SOL 2345 OW  0.821094 (nm)
> t: 1  139 SOL 2346 HW1  0.810919 (nm)
> t: 1  139 SOL 2347 HW2  0.771526 (nm)
> t: 1  7237 SOL 23640 HW1  0.997056 (nm)
> t: 1  11793 SOL 37307 OW  0.868929 (nm)
> t: 1  11793 SOL 37308 HW1  0.927205 (nm)
> t: 1  11793 SOL 37309 HW2  0.776699 (nm)
> t: 2  125 SOL 2303 OW  0.940527 (nm)
>
> In this
>
> t: 1  136 SOL 2336 OW  0.772373 (nm)
>
> does the 't' states the time frame, 136 SOL states the SOL molecule number
> and 2336 OW the residue contact from protein and the 0.772373 nm the
> distance between them.
>
> Thanks
>
>
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Re: [gmx-users] termini modification

[lina]

pdb2gmx -ter

On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj  wrote:
> Hello,
>
> I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
> terminal residues from NALA and CALA to normal ALA (just as middle
> residues). As the terminal selection option is not enabled with the amber
> ff, I am using the termini modification parameters with aminoacids.c.tdb.
> here is my code for the aminoacids.c.tdb
>
> [ COO- ]
>
> [ replace ]
> H    H    1.00800        0.27190
> N    N    14.01000    -0.41570
> CA    CT    12.01000    0.03370
> HA    H1    1.00800        0.08230
> C    C    12.01000    0.59730
> CB    CT    12.01        -0.1825
> HB1    HC    1.008        0.0603
> HB2    HC    1.008        0.0603
> HB3    HC    1.008        0.0603
>
> [ add ]
> 1    1    O    C    CA    N
>         O    16.0    -0.56790
>
> [ bonds ]
> C    O     1    0.12290        476976.0
>
> [ delete ]
> OC1
> OC2
>
>
> when I run pdb2gmx using this termini modification, everything works fine
> except the deletion of OC1 and OC2 atoms, the error which I get for this run
> as follows,
>
> Fatal error:
> Atom OC2 not found in residue seq.nr. 8 while adding atom
>
>
> any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
> delete ] option with the aminoacids.c.tdb file, it works fine by adding the
> O atom to the terminal residue including the presence of OC1 and OC2 atoms.
> first I am trying to modify the c terminal residue.
>
> Regards,
> vijay.
>
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Re: [gmx-users] Regarding g_sham

[lina]

On Sat, Aug 13, 2011 at 3:36 PM, bipin singh  wrote:
> Hello,
> Please let me know from where can I get the full description of g_sham
> module, as the manual does not
> provide full description of the options for g_sham in gromacs.
> for e.g I want to know the description about the following options in g_sham:
>
> -map
> -ls3
> -mdata
>

Sorry, I am not sure what's kind of "full description" you expect,

Try:

g_sham -h

or

man g_sham

>
>
> --
> ---
> Regards,
> Bipin Singh
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Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'

[lina]

On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers
 wrote:
> Dear all,
>
> searching for the mentioned error message I found a bug report for mdrun. It
> seemed to be fixed, but in my setup it appears again and I am not sure if I
> could do something about it.
>
> I did not attach the tpr file since it is bounced by the mailing list and
> I'd like to get at least a hint without waitng for approval of the rejected
> mail. :)
> The simulation crashes with 64 CPUs after step 11237000 with the following
> entry in the log file:
>
> ---
> Program mdrun, VERSION 4.5.4
> Source code file:
> /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352
>
> Software inconsistency error:
> One or more interactions were multiple assigned in the domain decompostion
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> That means that the simulation already ran for some time. I could also
> finish some runs successfully with the very same topology but different
> simulation parameters.
>
> For any help or hints how I could fix it I would be grateful.

Have you tried to re-submit it, use the -cpi state.cpt -append

and see whether it can continue or not?

>
> Best regards
>
>
> Sebastian
>
> --
> _
>
> Sebastian Breuers               Tel: +49-221-470-4108
> EMail: breue...@uni-koeln.de
>
> Universität zu Köln             University of Cologne
> Department für Chemie           Department of Chemistry
> Organische Chemie               Organic Chemistry
>
> Greinstraße 4                   Greinstraße 4
> Raum 325                        Room 325
> D-50939 Köln                    D-50939 Cologne, Federal Rep. of Germany
> _
>
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