[gmx-users] Error in installation
Hi I have been trying to install Gromacs on ubuntu. After make command I got the following error */usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC* */usr/local/lib/libfftw3f.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd.la] Error 1* *make[3]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* *ankit@ubuntu:~/gromacs/gromacs-4.5.5$ * How can I solve this error? Thanks Kumud Agarwal -- gmx-users mailing listgmx-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
RE: [gmx-users] questions on distance restraints
Dear Tsjerk, Thanks very much indeed for confirming this, really appreciate it. I will do as you suggest to have a more thorough check. Best wishes, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, January 18, 2012 1:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] questions on distance restraints Hi Huiwen, Your approach seems good. Information about the distance restraints will be printed in the log file from mdrun, or can be extracted from the .edr file. You can also work your way through the information in the .tpr file given by gmxdump to see if they are indeed properly defined. Cheers, Tsjerk On Jan 18, 2012 1:46 AM, NG HUI WEN huiwen...@nottingham.edu.mymailto:huiwen...@nottingham.edu.my wrote: Dear gmxusers, I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance. I am trying to apply distance restraints to my protein. Below was what I did: -use genrestr to create my ca_disre.itp genrestr -f membedded_em.gro -o ca_disre.itp -disre (pop-up prompt: CA atoms selected) -in my mdp file I added this line near the top: define = -DDISRES -my top file looks like that ; Include forcefield parameters #include gromos53a6_lipid.ff/forcefield.itp ;Include Protein Topology #include A2a.itp ; Include Position restraint file #ifdef DISRES #include ca_disre.itp #endif ; #ifdef POSRES #include posre.itp #endif ; ;Include POPC topology #include popc.itp #ifdef LIPID_POSRES #include lipid_posre.itp #endif ;Include water topology #include gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6_lipid.ff/ions.itp [ system ] ; Name Protein and POPC and Water [ molecules ] ; Compound#mols Protein_chain_X 1 POPC 327 SOL 24767 CL 11 The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)? I had checked the mdout.mdp file define = -DDISRES was there... wasn't sure how else I could check this. To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with disre_fc= 1 added to the mdp file. This time the atoms did not move as far away as previously observed. I have tried google-ing for the proper way to impose distance restraints but didn't find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong. Cheers for that! Best wishes, Huiwen This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with
AW: [gmx-users] Regarding trajectory file
Or you could use trjconv in a little script to convert the snapshots you
like to .pbd. Use the -b and -e flags to choose the respective time
points.
Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.
Good luck.
Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von aiswarya pawar
Gesendet: Mittwoch, 18. Januar 2012 07:53
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Regarding trajectory file
You can write this on VMD forum. Anyways you can try by doing this in
the Tcl console-
set sel [atomselect top solvent]
$sel get {x y z}
This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get for each time step.
Aiswarya
SERC Dept, IISc
Bangalore
On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:
Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and
solute at different time steps from the trajectory file (*.xtc). Can
anybody tell me how to extract the details using VMD or any other
viewer.
You're unlikely to get help for non-GROMACS software on this mailing
list. Check out manual section 7.4 for clues on what GROMACS tools might
help, and then section 8 and appendix D for more details.
Mark
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[gmx-users] option -r2 on g_hbond, a third HB citerion?
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard -- gmx-users mailing listgmx-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
[gmx-users] pb2gmx SS bond selection
Dear all, I'm using the option -ss to select the SS bonds I want to preserve when so problem occur with multiple bonds possible. The problem is that pdb2gmx asks me if I want to preserve the bound between an atom or not. It is very difficult to do this automatically. Is there a way to tell pdb2gmx which one I would like to preserve without using thoses question? Directly in the command line? Thank you. Pierre THEVENET -- gmx-users mailing listgmx-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
[gmx-users] mdrun-gpu error
Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-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
Re: AW: [gmx-users] Regarding trajectory file
Rausch, Felix wrote: Or you could use trjconv in a little script to convert the snapshots you like to .pbd. Use the –b and –e flags to choose the respective time points. Also see http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts for the use trjconv non-interactively. Or, more directly, just trjconv -dump. -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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Error in installation
On 18/01/2012 7:30 PM, kumud agarwal wrote: Hi I have been trying to install Gromacs on ubuntu. After make command I got the following error */usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC* See http://www.gromacs.org/Downloads/Installation_Instructions#Details_for_building_the_FFTW_prerequisite Mark */usr/local/lib/libfftw3f.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd.la http://libmd.la] Error 1* *make[3]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* *ankit@ubuntu:~/gromacs/gromacs-4.5.5$ * How can I solve this error? Thanks Kumud Agarwal -- gmx-users mailing listgmx-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
Re: [gmx-users] pb2gmx SS bond selection
pitheve...@free.fr wrote: Dear all, I'm using the option -ss to select the SS bonds I want to preserve when so problem occur with multiple bonds possible. The problem is that pdb2gmx asks me if I want to preserve the bound between an atom or not. It is very difficult to do this automatically. Is there a way to tell pdb2gmx which one I would like to preserve without using thoses question? Directly in the command line? http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts To do so requires you to know the order of a (potentially) large string of numbers before running the command, so it may or may not save you a whole lot of time, unless you're doing the exact same thing multiple times (which is unnecessary, since you'd be creating the same topology). Basically, you'd have to run pdb2gmx to get the sequence of responses, by which point, you no longer need the scripted version. -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 -- gmx-users mailing listgmx-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
Re: [gmx-users] option -r2 on g_hbond, a third HB citerion?
On 18/01/2012 8:35 PM, Mr Bernard Ramos wrote: Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off Apparently nobody knows. Someone will need to look in the code to find out - probably you :-). Good luck! Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] Error in installation
Hi, 1.method: You can install it from Synaptic package manager. 2.method: sudo apt-get install libfftw3-dev Later, in gromacs directory ./configure sudo make sudo make install sudo make mdrun sudo make links 2012/1/18 Mark Abraham mark.abra...@anu.edu.au On 18/01/2012 7:30 PM, kumud agarwal wrote: Hi I have been trying to install Gromacs on ubuntu. After make command I got the following error */usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC* See http://www.gromacs.org/Downloads/Installation_Instructions#Details_for_building_the_FFTW_prerequisite Mark */usr/local/lib/libfftw3f.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd.la] Error 1* *make[3]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* *ankit@ubuntu:~/gromacs/gromacs-4.5.5$ * How can I solve this error? Thanks Kumud Agarwal -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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
Re: [gmx-users] Regarding trajectory file
On 18.01.2012 07:31, Ravi Kumar Venkatraman wrote: Dear All, I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using In the directory of the xtc file, the (2'nd) command $ mkdir GRO $ trjconv -noh -novel -skip 1 -sep -nzero 4 -o GRO/out.gro will save every single frame of your simulation in a .gro file into a subdirectory GRO/ If you don't wan't every single frame, use -skip 2 in the above option to get every second frame. mwa -- gmx-users mailing listgmx-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
Re: [gmx-users] mdrun-gpu error
Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] mdrun-gpu error
Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] mdrun-gpu error
On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Pállszilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS usersgmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Chromophore residue patch in gromacs
Hi, I have been trying to attach the chromophore of GFP in charmm ff parameter files. The parameters have been obtained from a published article. After making the changes as per the documentation ( http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) , I am getting following error :- Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 51 The chromophore residue number is 66, I don't understand why there is an error for residue 51 . Please help me in rectifying this error .. Regards -- Bharat -- gmx-users mailing listgmx-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
Re: [gmx-users] Chromophore residue patch in gromacs
Are you crosslinking the chromophore to an atom in residue 51? Can you generate a correct topology without the chromophore as a check? On 2012-01-19 11:50:37AM +0900, bharat gupta wrote: Hi, I have been trying to attach the chromophore of GFP in charmm ff parameter files. The parameters have been obtained from a published article. After making the changes as per the documentation ( http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) , I am getting following error :- Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 51 The chromophore residue number is 66, I don't understand why there is an error for residue 51 . Please help me in rectifying this error .. Regards -- Bharat -- gmx-users mailing listgmx-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 listgmx-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
[gmx-users] Question about Andersen thermostat
Dear All, We are doing a simulation for ice melting in Efield with thermostat. We would like use Andersen thermostat to couple the temperature but found that it is not implemented yet, even on the latest version of GROMACS. Is there any way we can employ Andersen thermostat directly on GROMACS or we need to write extra scripts by ourselves? Many thanks, Alex-- gmx-users mailing listgmx-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
Re: [gmx-users] Chromophore residue patch in gromacs
On 19/01/2012 3:17 PM, bharat gupta wrote: No. I am not trying to crosslink the chromophore with nay residue but I have linked it with neighboring Valine(68) and Leucine(64) by specifying the bonds in specbond.dat file. You still have to go and look at residue 51 and see what is going on. The problem can be independent of the chromophore, as Peter was suggesting. Mark On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai p...@uab.edu mailto:p...@uab.edu wrote: Are you crosslinking the chromophore to an atom in residue 51? Can you generate a correct topology without the chromophore as a check? On 2012-01-19 11:50:37AM +0900, bharat gupta wrote: Hi, I have been trying to attach the chromophore of GFP in charmm ff parameter files. The parameters have been obtained from a published article. After making the changes as per the documentation ( http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) , I am getting following error :- Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 51 The chromophore residue number is 66, I don't understand why there is an error for residue 51 . Please help me in rectifying this error .. Regards -- Bharat -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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 mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-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
[gmx-users] getting rid of PBC, completely
Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions ). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-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
Re: [gmx-users] getting rid of PBC, completely
Hi Chadan, You should stop after your second step, removing jumps. Don't center. And definitely don't put the system in the box, as that exactly undoes removal of jumps. Cheers, Tsjerk On Thu, Jan 19, 2012 at 7:39 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] getting rid of PBC, completely
On 19/01/2012 5:39 PM, Chandan Choudhury wrote: Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. You can't get rid of PBC, you can only manage it. The question reduces what you want to see if a molecule diffuses across the periodic boundary from near one end of the polymer to the other end. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc So here you said let molecules diffuse away from the solute. #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom ... and now you said take all the atoms and put them back in the box, creating jumps whenever one crosses the boundaries. Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Don't simulate with them :-P Is your analysis technique sound for the periodic case? Mark -- gmx-users mailing listgmx-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
