Re: [gmx-users] GMX_MAXCONSTWARN variable
Am Samstag, den 08.11.2008, 20:02 -0800 schrieb zazeri: I'd like to know if the GMX_MAXCONSTWARN variable only turn off lincs warnings or turn off the lincs algorithm fully? And how I do define this variable; I imagine something like it at bashrc: export GMX_MAXCONSTWARN=$GMX_MAXCONSTWARN:-1 I have export GMX_MAXCONSTRWARN=-1 in a specific profile file of mine. I think your construct is used, e.g. to append a path to the $PATH variable. Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] version gromacs
Dear justin thank you.No ,because nothing enough free spce I must do MD on another pc with version 3,3,1.but I donot get problem and my result is good.what is your idea?Is it right.? -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] version gromacs
shahrbanoo karbalaee wrote: Dear justin thank you.No ,because nothing enough free spce I must do MD on another pc with version 3,3,1.but I donot get problem and my result is good.what is your idea?Is it right.? If you have to use version 3.3.1 on that particular machine, use it for all steps (EM, PR, MD). It is better to be consistent, as I told you before. Otherwise, upgrade the Gromacs version on the machine that is running those calculations to 3.3.3, like the machine where you are doing EM. Otherwise, just upgrade everything entirely to the newest version :) -Justin -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is gromacs-4.0.2 finally released?
Hi all, I found that gromacs-4.0.2.tar.gz under ftp.gromacs.org/pub/gromacs for a while, but now it is no longer there. Is this version finally and officially released? Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FATAL ERROR: x2top
Dear gmxuser I wan to make itp file to use opls forcefield. When I use x2top, I took the following error: Fatal error: No forcefield type for atom CAA (1) with 4 bonds what should be the problem? thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parameters
Dear users, I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and the following parameters (only a few are given): ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 125000 comm-mode= Linear nstcomm = 1 nstlist = 10 ns-type = Grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 I recently noticed from the manual that the nstlist should be 5 with gromos 96 ff. I have a couple of questions. 1. should this be 5 with a 0.001 timestep or with a 0.002 timestep 2. As I have done a lot of work using these parameters I was really looking for some suggestions/advice as to whether I can use any of my data - I;m really clinging onto hope here! And as to how 'badly' this choice/mistake will have affected my work. Thanks, Les ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Water model = amber port to gromacs ? = OR Only SPC ?
Hi Can the TIP3P water model used under gromos 96 force field? Although the Amber_TIP3P.top can port to gromacs, it based on the amber99 force field. I read about the imcompatibility of any two force field parameters from different sources, such as amber99 and gromos96. Is Gromacs only limited to SPC water model? Or, where to get the TIP*P.top water model compatible of the gromos96 force field ? Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology
Dear all... How to draw the structure for ionic liquid and get their PDB file? For example, we can draw the struture by using PRODRG generation server and get their PDB file. So, any suggestion to draw the structure and get their PDB file without using PRODRG generation server? Thank you for your suggestion and information... Naimah Haron Graduate Research Assistant Department of Chemistry Universiti Putra Malaysia Malaysia ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Deuterium order parameter over area of membrane
Hi, I know that deuterium order parameter can be calculated by g_density but it calculate average deuterium order parameter of a type of lipid Vs. atom number of the tail of the lipid. But I want to calculate deuterium order parameter fluctuation over the area. i.e., I want to know to calculate Scd per area of the membrane. Could you tell me how to do it. Thanks, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] posre.itp
Bhawana Gupta wrote: hello everyone, Pls tell me from where i can get posre.itp means format of this file. Chapter 5 of the manual, like I said last time. Repeating the same questions doesn't help you look like someone worth donating time to helping :-) Here in one mail named topology, you had given solution for making pdb file from one other than PRODRG i.e. Build a small one by hand in a text editor (making sure the density is suitable and there won't be steric clashes across periodic boundaries), replicate it with genbox, and equilibrate. But sorry i didnot get it. So explain it by another way. Please do not combine threads. This makes it hard for people to follow discussions. I'm sorry you don't understand my instructions, but they are perfectly clear, and will work if you understand the file format you are creating. Unfortunately, nobody has yet managed to write a software package that can already do everything every user might want. Since, ionic liquids are outside the normal scope of GROMACS, it's not surprising that there is not immediate support for it. It would also be a poor idea for someone new to GROMACS to immediately try to do things outside of its normal scope - the learning curve would be very steep indeed. If by ionic liquids you mean aqueous solutions containing ions, then that's another matter. can we use PRODRG for making peptides with usual amino acid. Yes, caveat all the normal warnings about PRODRG. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] posre.itp
hello everyone, Pls tell me from where i can get posre.itp means format of this file. Here in one mail named topology, you had given solution for making pdb file from one other than PRODRG i.e. Build a small one by hand in a text editor (making sure the density is suitable and there won't be steric clashes across periodic boundaries), replicate it with genbox, and equilibrate. But sorry i didnot get it. So explain it by another way. can we use PRODRG for making peptides with usual amino acid. sorry i am asking u again about this. with regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: High frequency output slow down the simulation?
This is one reason why I developed the checkpointing script that is
available in the wiki under beginners - checkpointing_jobs
Often a cluster node allows you to write to ${TMPDIR} which creates a
unique directory that is actually local and then you can copy the
contents to your final storage space.
Chris.
-- original message --
Yang Ye wrote:
Writing on local or remote certainly makes a difference. How about
the speed with no output at all?
Absolutely. Depending on the cluster setup, the best option is often
along the lines of
1) Write to disk physically associated with the CPUs (IIRC for GROMACS,
preferably the disk associated with MPI node 0, where applicable).
2) Write minimally often for your needs - using XTC rather than TRR
output wherever high precision is not required.
3) Arrange for the file to be returned to more convenient or permanent
file space at the end of the job.
This last step might be as simple as adding some cp commands to your
batch script, or perhaps issuing some stage file out instructions to
your batch system.
Your first port of call should be the cluster administrator /
documentation for how best you should be doing these steps. We can't
help much there.
Mark
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[gmx-users] Gromacs 4 Scaling Benchmarks...
I was wondering if anyone could comment on these benchmark results for the d.dppc benchmark? Nodes Cutoff (ns/day) PME (ns/day) 4 1.331 0.797 8 2.564 1.497 16 4.5 1.92 32 8.308 0.575 64 13.5 0.275 128 20.093 - 192 21.6 - It seems to scale relatively well up to 32-64 nodes without PME. This seems slightly better than the benchmark results for Gromacs 3 on www.gromacs.org . Can someone comment on the magnitude of the performance hit and lack of scaling with PME is worrying me. For the PME runs, I set rlist,rvdw,rouloumb=1.2 and the rest set to the defaults. I can try it with some other settings, larger spacing for the grid, but I'm not sure how much more that would help. Is there a more standardized system I should use for testing PME scaling? This is with GNU compilers and parallelization with OpenMPI 1.2. I'm not sure what we're using for the FFTW The compute nodes are Dell m600 blades w/ 16GB of RAM and dual quad core Intel Xeon 3GHz processors. I believe it's all ethernet interconnects. Thanks, YQ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Thickness distribution over area of bilayer-membrane
Hi, I saw that average thickness can be measured by peak to peak distance of a electron density graph. This electron density can be calculated by g_density command. But g_density gives the average electron density of the membrane. So, I can get the average thickness of the membrane by subtracting peak to peak distance of the electron density graph. But I want to see how the thickness of the membrane is fluctuating over area. So, can you tell me how I can calculate the thickness of the membrane. Regards, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Water model = amber port to gromacs ? = OR Only SPC ?
Chih-Ying Lin wrote: Hi Can the TIP3P water model used under gromos 96 force field? Although the Amber_TIP3P.top can port to gromacs, it based on the amber99 force field. I read about the imcompatibility of any two force field parameters from different sources, such as amber99 and gromos96. Is Gromacs only limited to SPC water model? No. Or, where to get the TIP*P.top water model compatible of the gromos96 force field ? They're already there as tip*p.itp - see the contents of share/gromacs/top in your installation. You just need to #include the right file. Note that for the purposes of genbox, SPC and TIP3P are equivalent. IIRC there's some poking around you need to do with amber99, but you should check its documentation for what to do there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] missing of methyl at N-terminal
Bhawana Gupta wrote: hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. Terminology is important to get right. You were capping the *C-terminal* end with an *N-methyl*. * i m using forcefield ffgmx. That's a poor idea for anything other than a learning exercise. That force field has been deprecated for years. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: - Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574 Fatal error: atom N not found in residue 1ACE while combining tdb and rtp - This is my pdb file in text editor So what were your pdb2gmx command line and responses to prompts? You need to think carefully about why pdb2gmx might be looking for an N atom in your ACE residue that doesn't have one. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Spatial distribution
I am not sure what is going on in this case. You could try: which g_spatial to see what is being picked up. You could also try to move the g_spatial executable to its own directory and then execute g_spatial from that path: /new/path/to/executable/g_spatial -h ls /new/path/to/executable/g_spatial g_spatial Otherwise I am not sure what is going on. Are you sure that you didn't compile g_cluster under the name g_spatial by accident? Chris. -- original message -- HI Chris I followed the steps below and when i tried to run g_spatial it executed g_cluster instead. Even when i do g_spatial -h it looks like its being overwritten by g_cluster 1.I used make_ndx to create a group containing the atoms around which i want the SDF 2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur compact -pbc none 3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans 4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding NH2 cap to C terminal
sarbani chattopadhyay wrote: Hi, I want to add -NH2 to the c terminal end of my peptide. If I modify the C-terminal databse- -c.tdb , will it be possible to add -NH2 to the CO end of the last residue at the C terminal end. For some forcefields, yes. You need the forcefield to have parameters for (C-terminal) -C(O)-NH2. Not all of them do. Probably the ones that have it parameterized already have the terminus topologies in the database. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology
naimah haron naimah wrote: Dear all... How to draw the structure for ionic liquid and get their PDB file? For example, we can draw the struture by using PRODRG generation server and get their PDB file. So, any suggestion to draw the structure and get their PDB file without using PRODRG generation server? Build a small one by hand in a text editor (making sure the density is suitable and there won't be steric clashes across periodic boundaries), replicate it with genbox, and equilibrate. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Electron density over area
Hi, I know that electron density can be calculated by g_density. But I want to calculate electron density over area of the membrane so that I can analyze the fluctuation of the electron density with the area of the membrane. Could you tell me how to do it? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
