Re: [gmx-users] g_sham
My bad, I had a typo, try this one:
awk -v x=firstcoordmin -v y=secondcoordmin 'BEGIN{while(getline
first_coordinate_file_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}}NR0{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==y){print
$1}}}' second_coordinate_file_here.xvg
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba
nabajyoti.gosw...@gmail.com
Sent: Saturday, August 22, 2015 4:16 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sham
Dear Micholas,
The awk command that you have suggested as:
awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline
yourfile_first_coordinate_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==$y){print
$1}}' yourfile_second_coordinate_here.xvg
is not working. It says ^ unexpected newline or end of string. I have
supplied my coord1min, coord2min, yourfile_first_coordinate_here.xvg and
yourfile_second_coordinate_here.xvg.
can you please re-write the command with correct syntax please?
On Fri, Aug 14, 2015 at 10:44 AM, Naba nabajyoti.gosw...@gmail.com wrote:
Thank you very much Micholas.
I have actually done the second option. But I was uncertain whether I have
done are all nonsense.
From your replies it seems that I am quite close to fulfill my objectives.
Meanwhile, I am about to perform dPCA for those loops as you have suggested
in the previous mail.
Thanks a lot.
On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. smit...@ornl.gov
wrote:
Hi Naba,
I believe you would want to do your second option if you want to include
the contributions from all of the loops. If you are just interested in one
loop, then you would do each seperately. Rule-of-thumb for these
calculations are whatever group you use for the convariance matrix, is what
you should use for the 2D projection.
Hope that helps.
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Naba
nabajyoti.gosw...@gmail.com
Sent: Thursday, August 13, 2015 4:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sham
Thanks for the reply Micholas.
I read the special discussion on dPCA at your provided link. But that is a
fact of small peptide penta-alanine.
I actually completed a 100 ns simulation of a outermembrane protein (of
239
amino acid residues) with 284 DMPC molecules. The protein contains 4
extracellular loops of variable lengths and I want to study the dynamics
of
these loops. What I wanted to confirm is:
1. Is it all right if I extract covariance separately for each loops? OR,
2. Should I calculate covariance of index groups of my concerned loops and
then should I proceed to 2D projection (by g_anaeig)?
On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. smit...@ornl.gov
wrote:
1. Is it feasible to obtain free energy landscape (FEL) from a 2D
projection (using g_anaeig) of index groups (say some loop's atoms)
which
are used for the least squares fit in g_covar and then selecting index
group of elements that corresponds to the eigenvectors (say
Prot-masses)?
Or,
Should I calculate covariance (g_covar) of my concerned loops
separately
and then should I go for g_sham?
I am not sure if I understand, however, I think I may be able to help a
litttle. g_sham is just a histograming program that inverts the
resulting
histogram into energy space, so using a 2D projection is a legitimate
use.
Indeed what you are trying to do is very similar to the steps used in
dPCA
(see:
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
).
2. Is there any representative way to get the exact time point for the
corresponding minima obtained from g_sham?
If you have the time series for each of the coordinates used in the 2D
projection you just need to scan through the 2D timeseries for values
that
match the minimia. e.g. If in the g_sham a minima is at coordinates
(10,10)
than you need to scan through the timeseries of your coordinates:
time coord1 coord2
1 00
2 1 10
3 40 400
41025
...
...
5000 10 10
.
6000 1010
.
988908 10 10
where frames 988908, 5000, and 6000 are the ones you are looking for.
You
could extract these with
awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline
Re: [gmx-users] Membrane protein insertion
Hi, I used this method recently and I was experiencing the same errors. As Mark suggested, makes sure your protein survives an energy minimisation. My error was a result of poor preparation of the .pdb file before running pdb2gmx. My .itp file contained a long bond between the C and N termini of a dimer. IF you have any doubts, try running InflateGRO2 using a very small part of your protein (1 chain) and see if it works. Anthony On 24/08/2015 08:59, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Something isn't stable. Check that your membrane protein survives a vacuum EM (at least). And check your parameter settings for inflategro. Mark On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández yasser.almeida.hernan...@chemie.uni-hamburg.de wrote: Hi all, I want to insert a membrane protein into a model bilayer and I've tried several methods. The more straightforward seems to be Memembed, which gives an orientation to the membrane. On the other hand this method only outputs the membrane as dummy balls. How to translate this orientation to a model bilayer (DOPC, POPC)? On the other hand I've tried InflateGRO2 for this purpose and I got this error (following the tutorial in https://code.google.com/p/inflategro2/wiki/TutorialTolC ): Back Off! I just backed up ../1-topology/4hzuS_popc.top to ../1-topology/#4hzuS_popc.top.3# Will use a deflating factor of 0.925539817285086 to shrink the lipids back in 20 steps Deflating grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n inflated.ndx -o tmp.tpr -maxwarn 1 mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro - ERROR: Cannot open GRO file shrink.00.gro: No such file or directory The end of the log.out file is this: Fatal error: Too many LINCS warnings (1184) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem Any thoughts? Thanks in advance -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Coulomb barriers and Coulomb Softcore Potential
Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the electrostatic potential (Lennard Jones fully active). Considering energetic barriers, I would like to adjust the Coulomb Softcore Potential. Does this seem plausible and if so, how is the Coulomb Softcore Potential defined in Gromacs? Naden and Shirts provide a concept by equation (A.2) in Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 www.ift-bs.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Coulomb barriers and Coulomb Softcore Potential
Adjusting the soft core is a gigantic pain. I wouldn't recommend it, and it's likely not necesssary. What settings are you using now? Note that the manual describes how it is defined. Can you post the alchemical-analysis output for N/N_k? There's an analysis quirk we are looking at where the correlation times are measured to be longer than they actually are, though that is when LJ is changing and coul is turned off. Look at the time correlation for the variable that is changing -- does it look stationary, or does it look like it's changing slowly, or has just a few discrete steps? If the autocorrelation time is slow, then N/N_k actually is that long, and the code is doing it's job. On Mon, Aug 24, 2015 at 9:55 AM, Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the electrostatic potential (Lennard Jones fully active). Considering energetic barriers, I would like to adjust the Coulomb Softcore Potential. Does this seem plausible and if so, how is the Coulomb Softcore Potential defined in Gromacs? Naden and Shirts provide a concept by equation (A.2) in Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 www.ift-bs.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is dVremain/dl related to fep-lambdas?
That could be documented better. It is all of the changes in the molecule that are not explicitly occurring in their own lambda variable. For example, in setup 2, then all the changes have separate dhdl terms, so there is nothing left to be in dVremain/dl. Note that in setup 1) dVremain/dl is just the sum of the other three terms in setup 2). On Mon, Aug 24, 2015 at 3:55 AM, Igor Leontyev ileont...@ucdavis.edu wrote: Dear gmx-users, When I compute with gromacs-5.1 relative free energies using mixed topologies (i.e. by setting typeA, typeB, bond kA, kB ant etc) I see that some undocumented value dVremain/dl is printed in log- and xvg-files. Please, clarify the exact meaning of the dVremain/dl quantity. How it is used in dG computation? == Some Thoughts === Playing with different setup by setting parameters fep-lambdas, coul-lambdas, vdw-lambdas and bonded-lambdas, I figured out that dVremain/dl of Setup-1 (when set only fep-lambdas) is equal to sum of all dV/dl components of Setup-2 (when all coul-lambdas, vdw-lambdas and bonded-lambdas are set explicitly): dVremain/dl(1) = Vcoul/dl(2) + dVvdw/dl(2) + dVbonded/dl(2) Setup-1) # if in MDP-file ; coul-lambdas = 0.0 0.10 ; vdw-lambdas = 0.0 0.10 ; bonded-lambdas = 0.0 0.10 fep-lambdas = 0.0 0.10 # then dVremain/dl 1.52124e+03 #endif Setup-2) # if in MDP-file coul-lambdas = 0.0 0.10 vdw-lambdas = 0.0 0.10 bonded-lambdas = 0.0 0.10 fep-lambdas = 0.0 0.10 # then dVremain/dl dVcoul/dl dVvdw/dl dVbonded/dl 0.0e+00 1.56939e+03 -6.97050e+01 2.15596e+01 #endif === -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Heat autocorrelation function
Dear sir, How can i calculate the heat autocorrelation function in gromacs ? I want to calculate the thermal conductivity of noble gases. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Heat autocorrelation function
On 24/08/15 09:25, Sunil Ghimire wrote: Dear sir, How can i calculate the heat autocorrelation function in gromacs ? I want to calculate the thermal conductivity of noble gases. I guess you need to run NVE simulations and store the energies often, then compute the autocorrelation function of the temperature or kinetic energy. What is the exact equation? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Membrane protein insertion
Hi all, I want to insert a membrane protein into a model bilayer and I've tried several methods. The more straightforward seems to be Memembed, which gives an orientation to the membrane. On the other hand this method only outputs the membrane as dummy balls. How to translate this orientation to a model bilayer (DOPC, POPC)? On the other hand I've tried InflateGRO2 for this purpose and I got this error (following the tutorial in https://code.google.com/p/inflategro2/wiki/TutorialTolC ): Back Off! I just backed up ../1-topology/4hzuS_popc.top to ../1-topology/#4hzuS_popc.top.3# Will use a deflating factor of 0.925539817285086 to shrink the lipids back in 20 steps Deflating grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n inflated.ndx -o tmp.tpr -maxwarn 1 mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro - ERROR: Cannot open GRO file shrink.00.gro: No such file or directory The end of the log.out file is this: Fatal error: Too many LINCS warnings (1184) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem Any thoughts? Thanks in advance -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Membrane protein insertion
Hi, Something isn't stable. Check that your membrane protein survives a vacuum EM (at least). And check your parameter settings for inflategro. Mark On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández yasser.almeida.hernan...@chemie.uni-hamburg.de wrote: Hi all, I want to insert a membrane protein into a model bilayer and I've tried several methods. The more straightforward seems to be Memembed, which gives an orientation to the membrane. On the other hand this method only outputs the membrane as dummy balls. How to translate this orientation to a model bilayer (DOPC, POPC)? On the other hand I've tried InflateGRO2 for this purpose and I got this error (following the tutorial in https://code.google.com/p/inflategro2/wiki/TutorialTolC ): Back Off! I just backed up ../1-topology/4hzuS_popc.top to ../1-topology/#4hzuS_popc.top.3# Will use a deflating factor of 0.925539817285086 to shrink the lipids back in 20 steps Deflating grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n inflated.ndx -o tmp.tpr -maxwarn 1 mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro - ERROR: Cannot open GRO file shrink.00.gro: No such file or directory The end of the log.out file is this: Fatal error: Too many LINCS warnings (1184) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem Any thoughts? Thanks in advance -- Yasser Almeida Hernández PhD student Institute of Biochemistry and Molecular Biology Department of Chemistry University of Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Germany +49 40 42838 2845 yasser.almeida.hernan...@chemie.uni-hamburg.de office: Grindelallee 117, room 250c -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Script to submit the md simulations on cluster.
Hi,
No, we can't. Every cluster is set up differently. You have to consult your
local documentation and sysadmins. That said, shell scripts tend to prefer
NAME=value
ie without spaces
Mark
On Mon, Aug 24, 2015 at 7:28 AM Seera Suryanarayana paluso...@gmail.com
wrote:
Dear gromacs users,
I would like to submit the mdrun on cluster. I have written a shell script
for submission as following.
EXECUTABLE=./mdrun_mpi465
ARGUMENTS = -v -deffnm md_0_1.tpr
INPUT_FILES = file:///home/suryanarayana1599/md.mdp,
file:///home/suryanarayana1599/npt.cpt,
file:///home/suryanarayana1599/npt.gro,
file:///home/suryanarayana1599/md_0_1.tpr,
file:///home/suryanarayana1599/topol.top
OUTPUT_FILES = md_0_1.trr,md_0_1.xtc,md_0_1.cpt
STDIN_FILE = /dev/null
STDOUT_FILE = ${JOB_ID}.out
STDERR_FILE = ${JOB_ID}.err
REQUIREMENTS = HOSTNAME=ggblr.garudaindia.in(this is cluster name)
TYPE=mpi
NP = 10
OUTPUT_FILES = 2000
Could any one tell me that whether the script is right.
Thanks in Advance
Surya
Graduate student
India.
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[gmx-users] Is dVremain/dl related to fep-lambdas?
Dear gmx-users, When I compute with gromacs-5.1 relative free energies using mixed topologies (i.e. by setting typeA, typeB, bond kA, kB ant etc) I see that some undocumented value dVremain/dl is printed in log- and xvg-files. Please, clarify the exact meaning of the dVremain/dl quantity. How it is used in dG computation? == Some Thoughts === Playing with different setup by setting parameters fep-lambdas, coul-lambdas, vdw-lambdas and bonded-lambdas, I figured out that dVremain/dl of Setup-1 (when set only fep-lambdas) is equal to sum of all dV/dl components of Setup-2 (when all coul-lambdas, vdw-lambdas and bonded-lambdas are set explicitly): dVremain/dl(1) = Vcoul/dl(2) + dVvdw/dl(2) + dVbonded/dl(2) Setup-1) # if in MDP-file ; coul-lambdas = 0.0 0.10 ; vdw-lambdas = 0.0 0.10 ; bonded-lambdas = 0.0 0.10 fep-lambdas = 0.0 0.10 # then dVremain/dl 1.52124e+03 #endif Setup-2) # if in MDP-file coul-lambdas = 0.0 0.10 vdw-lambdas = 0.0 0.10 bonded-lambdas = 0.0 0.10 fep-lambdas = 0.0 0.10 # then dVremain/dl dVcoul/dl dVvdw/dl dVbonded/dl 0.0e+00 1.56939e+03 -6.97050e+01 2.15596e+01 #endif === -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories
Dear Justin Thanks for the reply. If that's the case what position of atoms the coordinates in trr file represents?. If I got you right, the coordinates in trr file neither get along with the mdrun generated gro file due to domain decomposition (hence broken molecules) nor with the trjconv treated gro file since, as you said, the same treatment with trjconv is required for coordinates in trr file. Many thanks Anu On Wed, Aug 19, 2015 at 12:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:22 AM, anu chandra wrote: Dear Gromacs users, I just noticed that during simulation 'mdrun' writes gro file in two formats - one with broken molecules at the boundaries and other one where surface molecules are perfectly wrapped. Interestingly, this difference in format depends on where I run the simulation - either in a cluster or in my local 8-core desktop machine. Using 'mdrun' in cluster gives gro file with broken molecules at the boundaries and my desktop workstation gives the one with complete molecules at the surface. Below is the mdp file I used for simulation in both case * define = -DPOSRES_MD ; integrator = md dt = 0.002 nsteps = 5 ; nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; pbc = xyz ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling= com *** May I know what is making this difference? Due to the presence of broken molecules, I failed to visualizing the trajectories (.trr file) using VMD. Though I could make a gro file with complete molecules at the boundaries using trjconv command, *trjconv -f input.gro -o ouput.gro -s input.tpr -pbc mol* the visualization of trr file with output.gro also shows long bond between atoms across the boundaries. Please help me to rectify this issue with visualizing the trr file. You need to process the .trr file the same way using trjconv. Accounting for periodicity effects is a routine first step after a run finishes. In server, following grommp and mdrun commands are used, *gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.topmpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5* Here, you're using domain decomposition (anything 8 cores). Broken molecules get written. and, in my desktop workstation following commands are used *gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.topgmx mdrun -nt 8 -deffnm MD5* Here, there is no DD. Molecules are whole. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lambada + InflateGRO2 and membrane protein simulation
Dear All, Is any on-line server related to Lambada + InflateGRO2, which can gives the PDB file of the target membrane protein for simulation, including the coordinates of the surrounding lipid bilaylayer molecules? I am looking forward to getting a reply from you. Best regards. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pairwise h-bonds
Sorry I had a typo in my previous email: I have used the -hbm and -hbn option (not the -m as it does not exist). The problem is however that this option gives me the h-bonds for each residues of group 1 to _any_ residue of group 2 and not the pairwise h-bonds between all members of group 1 and group 2. i.e. it gives a 100x1000 matrix instead of a 100x100x1000 matrix. I guess I am not the first person enountering this problem so there must be a quite simple solution got get all pairwise h-bonds but I can't figure it out ... Best, Morpheus Erik Marklund erik.marklund at chem.ox.ac.uk Sat Aug 22 22:03:26 CEST 2015 Previous message: [gmx-users] pairwise h-bonds Dear Morpheus, Try the -hbn and -hbm options. The latter generates a similar matrix and the former is essentially a dictionary to that matrix. Kind regards, Erik On 21 Aug 2015, at 12:45, bernhard morpheus.sommer2008 at gmail.com wrote: Dear Gromacs users, I was wondering about the best way of obtaining pairwise h-bonds of certain residues. I got about 100 residues of interest and 1000 simulation frames. I would like to get the h-bonds at each timeframe between each pair of residues. i.e. a matrix with 100x100x1000. At the moment I have created an index group for each residue and run the pairwise h-bond calculations in two nested loops via a perl script. The problem is that this takes long and also creates 10 000 000 files on the harddisk which I then need to parse with another skript. Is there an easier way? I have also tried to use the -m option with protein and protein as input groups but this also those not give the pairwise h-bonds but rather the cumulative ones per residue against all 100 residues. Can anyone give me a hint? Cheers, Morpheus -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulations of ice beginning to spin
The box is defined by numbers at the last line of the GRO file. The point is that we do not know what happens with the box definition during the simulation. From what I could see at the final snapshot, the box in gromacs became cubic (based on location of molecules). On Mon, Aug 24, 2015 at 5:02 PM, Nathan K Houtz nho...@purdue.edu wrote: Thanks for your reply. How do I get gromacs to recognize that I want a triclinic box? I thought it was simply defined in the .gro file (as VMD recognizes). I know I can use gmx editconf to modify the gro file to define a triclinic box, but do I need anything in my input file? Thanks, Nathan - Original Message - From: Vitaly V. Chaban vvcha...@gmail.com To: gmx-users gmx-us...@gromacs.org Sent: Sunday, August 23, 2015 10:36:12 AM Subject: Re: [gmx-users] simulations of ice beginning to spin I suggest you to make a movie... Maybe, indeed, something is wrong with triclinic box definition (?) This not a rotation problem, since your crystal is outside the box at the end. Thus, the box which VMD drew is not the box which gromacs used during dynamics. On Fri, Aug 21, 2015 at 9:13 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello Eric, Thanks for your reply. I actually had made a mistake there, so that was a good catch. I used Linear instead of Angular to constrain movement, so gromacs actually wasn't fixing the rotation. However, I fixed it and redid the simulations and I'm still getting very nearly the same results. Does anything else come to mind? Thanks for your help, Nathan Houtz - Original Message - From: Eric Smoll ericsm...@gmail.com To: gmx-us...@gromacs.org Sent: Thursday, August 20, 2015 5:53:18 PM Subject: Re: [gmx-users] simulations of ice beginning to spin Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations in NPT with the Parrinello-Rahman Barostat. It did not solve the rotation problem. Both outputs looked very similar to the results from NVT. In addition, the corners of the cubic simulation still became disordered. That's the only update I have. Please see below for further details. Thanks! Regards, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gromacs org gmx-users gromacs.org_gmx-users@maillist.sys.kth.se Sent: Thursday, August 13, 2015 10:57:43 PM Subject: simulations of ice beginning to spin Hello, I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both simulations seem to have developed some rotation spontaneously and I'd like to know if I can control that somehow. I'm also simulating one in a triclinic box but the output gro file appears cubic. I'm not sure if I should be concerned about that or not. Lastly, the Ice Ic structure begins to fall apart during my simulation and I don't think it should. I'd appreciate help on any of these matters. Here are some more details: Ice Ih is done in a triclinic box, and originally looks like this: http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model, constrained by shake, and simulate it in NVT for 1,000,000 time steps (2 ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if gromacs has correctly applied the triclinic box, as it appears that periodic boundary conditions have turned it into a cube. VMD is showing the box described by the .gro file. Secondly, it has been rotated, at least a few degrees, about the z axis. It did not noticeably rotate about the x or y axes. I'm not sure how to explain how the simulation would develop any angular momentum. In my .mdp file, I have gromacs get rid of angular momentum every 100 steps, but I don't think it should develop any in the first place. Any advice? The other simulation, ice ic, didn't go quite as well. Here is the original orientation, viewed from one of the corners: http://imgur.com/i0ncpju (I realize the orthographic projections make it harder to see the actual structure, but they make it easier to see unique patterns from various angles, which I'm trying to use to determine how it has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3. The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure I've got the exact corresponding orientation in this view here, but I believe it is. It's looking down the x-axis this time. This simulation got rotated
Re: [gmx-users] simulations of ice beginning to spin
On 8/24/15 4:02 PM, Nathan K Houtz wrote: Thanks for your reply. How do I get gromacs to recognize that I want a triclinic box? I thought it was simply defined in the .gro file (as VMD recognizes). I know I can use gmx editconf to modify the gro file to define a triclinic box, but do I need anything in my input file? mdrun always uses a triclinic representation of any unit cell it is given. What you're seeing is just a visualization effect from re-wrapping. Process with trjconv (-pbc nojump, -pbc mol, or some such sequence of commands). -Justin Thanks, Nathan - Original Message - From: Vitaly V. Chaban vvcha...@gmail.com To: gmx-users gmx-us...@gromacs.org Sent: Sunday, August 23, 2015 10:36:12 AM Subject: Re: [gmx-users] simulations of ice beginning to spin I suggest you to make a movie... Maybe, indeed, something is wrong with triclinic box definition (?) This not a rotation problem, since your crystal is outside the box at the end. Thus, the box which VMD drew is not the box which gromacs used during dynamics. On Fri, Aug 21, 2015 at 9:13 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello Eric, Thanks for your reply. I actually had made a mistake there, so that was a good catch. I used Linear instead of Angular to constrain movement, so gromacs actually wasn't fixing the rotation. However, I fixed it and redid the simulations and I'm still getting very nearly the same results. Does anything else come to mind? Thanks for your help, Nathan Houtz - Original Message - From: Eric Smoll ericsm...@gmail.com To: gmx-us...@gromacs.org Sent: Thursday, August 20, 2015 5:53:18 PM Subject: Re: [gmx-users] simulations of ice beginning to spin Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations in NPT with the Parrinello-Rahman Barostat. It did not solve the rotation problem. Both outputs looked very similar to the results from NVT. In addition, the corners of the cubic simulation still became disordered. That's the only update I have. Please see below for further details. Thanks! Regards, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gromacs org gmx-users gromacs.org_gmx-users@maillist.sys.kth.se Sent: Thursday, August 13, 2015 10:57:43 PM Subject: simulations of ice beginning to spin Hello, I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both simulations seem to have developed some rotation spontaneously and I'd like to know if I can control that somehow. I'm also simulating one in a triclinic box but the output gro file appears cubic. I'm not sure if I should be concerned about that or not. Lastly, the Ice Ic structure begins to fall apart during my simulation and I don't think it should. I'd appreciate help on any of these matters. Here are some more details: Ice Ih is done in a triclinic box, and originally looks like this: http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model, constrained by shake, and simulate it in NVT for 1,000,000 time steps (2 ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if gromacs has correctly applied the triclinic box, as it appears that periodic boundary conditions have turned it into a cube. VMD is showing the box described by the .gro file. Secondly, it has been rotated, at least a few degrees, about the z axis. It did not noticeably rotate about the x or y axes. I'm not sure how to explain how the simulation would develop any angular momentum. In my .mdp file, I have gromacs get rid of angular momentum every 100 steps, but I don't think it should develop any in the first place. Any advice? The other simulation, ice ic, didn't go quite as well. Here is the original orientation, viewed from one of the corners: http://imgur.com/i0ncpju (I realize the orthographic projections make it harder to see the actual structure, but they make it easier to see unique patterns from various angles, which I'm trying to use to determine how it has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3. The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure I've got the exact corresponding orientation in this view here, but I believe it is. It's looking down the x-axis this time. This simulation got rotated much worse. Here are the before and after views looking down the z-axis, just like I showed for the ice Ih above: http://imgur.com/a/LRQR3.
Re: [gmx-users] calculate avarage and maximum non-bonded energy between energy groups
1) g_energy 2) g_analyze -f energy.xvg 3) Divide by 3 I do not know the physical sense of the maximum interaction energy. On Mon, Aug 24, 2015 at 4:25 PM, Tushar Ranjan Moharana tusharranjanmohar...@gmail.com wrote: Hi everyone, I want to calculate the average and if possible maximum non-bonded energy between different energy groups. I used gmx energy whose out put was energy vs time. I want different energy groups in X axix and energy (average and/or maximum) in Y axis. A matrix of N X N describing energy (average and/or maximum) between energy groups is also fine. (where N is number of energy group). I tried gmx enemat but it ends with following error *Opened FOA2_lip_pull.edr as single precision energy fileWill read groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energyfileWARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy fileWARNING! could not find group Coul-SR:Protein-Non-protein (0,1)in energyfileWARNING! could not find group LJ-SR:Protein-Non-protein (0,1)in energy filegroup 1WARNING! could not find group Coul-SR:Non-protein-Non-protein(1,1)in energy fileWARNING! could not find group LJ-SR:Non-protein-Non-protein (1,1)in energyfileWill select half-matrix of energies with 0 elementsLast energy frame read 1400 time 1400.000Will build energy half-matrix of 2 groups, 0 elements, over 1401 framesSegmentation fault (core dumped)* I tried 4.6.7 version and install GROMACS in debug mode but nothing worked for me. Can anybody suggest me something. Little hint will also be helpful. Thanks a lot in advance. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories
On 8/24/15 5:39 AM, anu chandra wrote: Dear Justin Thanks for the reply. If that's the case what position of atoms the coordinates in trr file represents?. If I got you right, the coordinates in trr file neither get along with the mdrun generated gro file due to domain decomposition (hence broken molecules) nor with the trjconv treated gro file since, as you said, the same treatment with trjconv is required for coordinates in trr file. I don't really understand the question, but the generic answer is: mdrun doesn't care about our visualization convenience. The physics don't depend on molecules being represented as whole so it does not waste time reconstructing them to write them to the trajectory. That's what trjconv is for - processing *any* trajectory or coordinate file that is broken across PBC. Your input coordinates were probably whole, so in order to visualize the trajectory, you need to use trjconv to process the .trr suitably. There are tips on the GROMACS website and in about half a million posts in the list archive on this. -Justin Many thanks Anu On Wed, Aug 19, 2015 at 12:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:22 AM, anu chandra wrote: Dear Gromacs users, I just noticed that during simulation 'mdrun' writes gro file in two formats - one with broken molecules at the boundaries and other one where surface molecules are perfectly wrapped. Interestingly, this difference in format depends on where I run the simulation - either in a cluster or in my local 8-core desktop machine. Using 'mdrun' in cluster gives gro file with broken molecules at the boundaries and my desktop workstation gives the one with complete molecules at the surface. Below is the mdp file I used for simulation in both case * define = -DPOSRES_MD ; integrator = md dt = 0.002 nsteps = 5 ; nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; pbc = xyz ; tcoupl = Nose-Hoover tc_grps = Protein POPC CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC CL_SOL ; refcoord_scaling= com *** May I know what is making this difference? Due to the presence of broken molecules, I failed to visualizing the trajectories (.trr file) using VMD. Though I could make a gro file with complete molecules at the boundaries using trjconv command, *trjconv -f input.gro -o ouput.gro -s input.tpr -pbc mol* the visualization of trr file with output.gro also shows long bond between atoms across the boundaries. Please help me to rectify this issue with visualizing the trr file. You need to process the .trr file the same way using trjconv. Accounting for periodicity effects is a routine first step after a run finishes. In server, following grommp and mdrun commands are used, *gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.topmpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5* Here, you're using domain decomposition (anything 8 cores). Broken molecules get written. and, in my desktop workstation following commands are used *gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.topgmx mdrun -nt 8 -deffnm MD5* Here, there is no DD. Molecules are whole. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] simulations of ice beginning to spin
Thanks for your reply. How do I get gromacs to recognize that I want a triclinic box? I thought it was simply defined in the .gro file (as VMD recognizes). I know I can use gmx editconf to modify the gro file to define a triclinic box, but do I need anything in my input file? Thanks, Nathan - Original Message - From: Vitaly V. Chaban vvcha...@gmail.com To: gmx-users gmx-us...@gromacs.org Sent: Sunday, August 23, 2015 10:36:12 AM Subject: Re: [gmx-users] simulations of ice beginning to spin I suggest you to make a movie... Maybe, indeed, something is wrong with triclinic box definition (?) This not a rotation problem, since your crystal is outside the box at the end. Thus, the box which VMD drew is not the box which gromacs used during dynamics. On Fri, Aug 21, 2015 at 9:13 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello Eric, Thanks for your reply. I actually had made a mistake there, so that was a good catch. I used Linear instead of Angular to constrain movement, so gromacs actually wasn't fixing the rotation. However, I fixed it and redid the simulations and I'm still getting very nearly the same results. Does anything else come to mind? Thanks for your help, Nathan Houtz - Original Message - From: Eric Smoll ericsm...@gmail.com To: gmx-us...@gromacs.org Sent: Thursday, August 20, 2015 5:53:18 PM Subject: Re: [gmx-users] simulations of ice beginning to spin Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations in NPT with the Parrinello-Rahman Barostat. It did not solve the rotation problem. Both outputs looked very similar to the results from NVT. In addition, the corners of the cubic simulation still became disordered. That's the only update I have. Please see below for further details. Thanks! Regards, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gromacs org gmx-users gromacs.org_gmx-users@maillist.sys.kth.se Sent: Thursday, August 13, 2015 10:57:43 PM Subject: simulations of ice beginning to spin Hello, I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both simulations seem to have developed some rotation spontaneously and I'd like to know if I can control that somehow. I'm also simulating one in a triclinic box but the output gro file appears cubic. I'm not sure if I should be concerned about that or not. Lastly, the Ice Ic structure begins to fall apart during my simulation and I don't think it should. I'd appreciate help on any of these matters. Here are some more details: Ice Ih is done in a triclinic box, and originally looks like this: http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model, constrained by shake, and simulate it in NVT for 1,000,000 time steps (2 ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if gromacs has correctly applied the triclinic box, as it appears that periodic boundary conditions have turned it into a cube. VMD is showing the box described by the .gro file. Secondly, it has been rotated, at least a few degrees, about the z axis. It did not noticeably rotate about the x or y axes. I'm not sure how to explain how the simulation would develop any angular momentum. In my .mdp file, I have gromacs get rid of angular momentum every 100 steps, but I don't think it should develop any in the first place. Any advice? The other simulation, ice ic, didn't go quite as well. Here is the original orientation, viewed from one of the corners: http://imgur.com/i0ncpju (I realize the orthographic projections make it harder to see the actual structure, but they make it easier to see unique patterns from various angles, which I'm trying to use to determine how it has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3. The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure I've got the exact corresponding orientation in this view here, but I believe it is. It's looking down the x-axis this time. This simulation got rotated much worse. Here are the before and after views looking down the z-axis, just like I showed for the ice Ih above: http://imgur.com/a/LRQR3. With such a large number of timesteps, I cannot output enough frames in the trajectory file to view this as a smooth movie and ide ntify exactly when and why these rotations happen. It's more like a very long and rapid
[gmx-users] calculate avarage and maximum non-bonded energy between energy groups
Hi everyone, I want to calculate the average and if possible maximum non-bonded energy between different energy groups. I used gmx energy whose out put was energy vs time. I want different energy groups in X axix and energy (average and/or maximum) in Y axis. A matrix of N X N describing energy (average and/or maximum) between energy groups is also fine. (where N is number of energy group). I tried gmx enemat but it ends with following error *Opened FOA2_lip_pull.edr as single precision energy fileWill read groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energyfileWARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy fileWARNING! could not find group Coul-SR:Protein-Non-protein (0,1)in energyfileWARNING! could not find group LJ-SR:Protein-Non-protein (0,1)in energy filegroup 1WARNING! could not find group Coul-SR:Non-protein-Non-protein(1,1)in energy fileWARNING! could not find group LJ-SR:Non-protein-Non-protein (1,1)in energyfileWill select half-matrix of energies with 0 elementsLast energy frame read 1400 time 1400.000Will build energy half-matrix of 2 groups, 0 elements, over 1401 framesSegmentation fault (core dumped)* I tried 4.6.7 version and install GROMACS in debug mode but nothing worked for me. Can anybody suggest me something. Little hint will also be helpful. Thanks a lot in advance. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Randomly alter pdb start coordinates
There is mentioned that for re-running an MD run for better statistics, it can be good to change starting coordinates, besides the seed, is there a gmx command which is used for randomly change starting coordinates of a pdb file? I need such a command or script for a PBS script which automatically goes through all gmx setup commands to start and run an arbitrary number of following MD production runs, assumed that all steps are working. I've also made it to replicate and change seeds automatically for velocity generation for three seeds, starting automatically. So three tests started with one bash script, and one clean-up script resetting everything. Thanks, Henry Wittler Phd in Molecular modelling group (Brian J. Smith) Department of Chemistry, La Trobe University, Melbourne, Australia Tel: 0432901627 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Heat autocorrelation function
I want to use green- kubo formalism , which uses the integral of autocorelation of heat flux J to calculate thermal conductivity. On 24 Aug 2015 13:25, David van der Spoel sp...@xray.bmc.uu.se wrote: On 24/08/15 09:25, Sunil Ghimire wrote: Dear sir, How can i calculate the heat autocorrelation function in gromacs ? I want to calculate the thermal conductivity of noble gases. I guess you need to run NVE simulations and store the energies often, then compute the autocorrelation function of the temperature or kinetic energy. What is the exact equation? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Single point energy calculations
Hello all, I am trying to calculate the single point energies of my system (a nucleic acid and a nanoparticle) to ultimately estimate the E(interaction). I am following this paper. http://ac.els-cdn.com/S0045653513001215/1-s2.0-S0045653513001215-main.pdf?_tid=cc0e4256-4add-11e5-8426-0aab0f26acdnat=1440475397_d1db3b13c45b5048a7722828548fb29e It was written that Eint= Etot- (EC60+ELOA) Where ETOT is the potential energy of the LOA-C60 system and E60 and ELOA are the single point energies obtained by stripping the LOA or the C60 from the equilibrium geometries of the LOA-C60 system. I have no idea how to calculate this single point energy. I have checked some of the discussion threads in GROMACS archive and also the single point webpage of GROMACS http://www.gromacs.org/Documentation/How-tos/Single-Point_Ene http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Regarding this I have some questions. 1. Is the .tpr file fed to grompp with -rerun generated by using a .top file consist only of the structure in the configuration.pdb file? 2. What parameters one should use in the corresponding .mdp file? 3. In some of the discussions I saw people used minim.mdp as well as md.mdp files with nsteps= 0. Which one to consider? 4. After the mdrun I am supposed to get am .edr file. Is the single point energy correspond to the potential energy in it or is it explicitly written elsewhere ( .log file) or is it some other energy term? I would appreciate any sort of help. I have never done single point energy calculations using MD simulations and sorry for asking much. Thanks and regards, Soumadwip Ghosh Senior Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
