Re: [gmx-users] QMMM

Good luck. I followed the instructions and was not successful. On Tue, Mar 8, 2011 at 12:48 AM, Haresh wrote: > Hello everyone, > > I want install gromacs with mopac7 for qmmm. > > Can you guide me for installation procedure > > Thank you. > > > -- > gmx-users mailing listgmx-users@gromacs.o

[gmx-users] GPU GROMACS

Is anyone working on a build GROMACS with CUDA other than the OpenMM project? I would like to build this with explicit solvents and as I understand it, OpenMM is implicit. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] Checkpointing

, Feb 2, 2010 at 6:18 PM, Mark Abraham >>  wrote: >>> >>> >>> - Original Message - >>> From: Jack Shultz >>> Date: Wednesday, February 3, 2010 2:36 >>> Subject: [gmx-users] Checkpointing >>> To: Discussion list for GROMACS

Re: [gmx-users] Checkpointing

I will try it without the checkpointing flags. If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists. On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham wrote: > > > - Original Message - > From: Jack Shultz > Date: W

[gmx-users] Checkpointing

We have mdrun integrated into our distributed computing project. When your users suspend or close the manger it checkpoints, so when they open again it continues mdrun where it left off. However, when users reboot, it starts from the beginning. We are using this command line to execute the work. m

Re: [gmx-users] Re: including a custom itp file in topology

I confess I don't know the difference between rtp and itp. What I was hoping was an easier way to generate topologies for complexes that have non-standard residue names like LIG. Alan's acpypi works. You just have to do some extra scripting. But it seems like pdb2gmx should have a way to load the f

[gmx-users] including a custom itp file in topology

Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand usin

[gmx-users] Missing Residues are list ind pdb file

I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the non-standard residues. Re-named n-terminal and c-terminal residues. Took out connects because that worked last time though I'm uncertain if connect really maters. Another issue with preping a protein. Its says I a missing H and HA

Re: [gmx-users] Unstable Minimizations

of the CYS residues involved in the disulfide bonds to CYS2. On Mon, Jan 11, 2010 at 11:57 AM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: > >> Well some of the problems in the log relate to unresolved exceptions >> processing the ligands, those ligands are skipped.

Re: [gmx-users] Unstable Minimizations

innappropriate atoms that I should remove? On Sun, Jan 10, 2010 at 9:58 PM, Justin A. Lemkul wrote: > > > On 1/10/10 9:47 PM, Jack Shultz wrote: > >> Thanks Justin, >> I went back to the original pdb files. These were conformations of the >> same protein d

Re: [gmx-users] Unstable Minimizations

max= 2.82196e+12, atom= 19392 Its not clear to me what we should do to correct this structures...maybe Andrey has some input. http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul wrote: > > > On 1/10/10 5:18 PM, Jack Shultz w

[gmx-users] Unstable Minimizations

I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing. http://boinc.drugdiscoveryathome.com/*em_restrained_rcs_md

[gmx-users] Mopac integration with gromacs

I am trying to use one of the free versions of mopac. I read there are some problems with mopac 7 and mopac 6 gives better results. In any case I am having trouble compiling either one. Has anyone had success with it? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-user

Re: [gmx-users] trouble minimizing structure with mdrun

maybe I should go directly from pdb2gmx to grompp seeing as I have already solvated and ionized the protein in VMD. On Mon, Jan 4, 2010 at 8:04 PM, Jack Shultz wrote: > I did a little more checking on the structures, I notice the results > from genion move part of the protein far outsi

Re: [gmx-users] trouble minimizing structure with mdrun

I did a little more checking on the structures, I notice the results from genion move part of the protein far outside the solvent box. I shall try this without the genion step I put all the files in the working directory for this preperation in a zip archive under http://boinc.drugdiscoveryathome.

Re: [gmx-users] Dead Link or Restricted Access to link

Thanks! On Mon, Jan 4, 2010 at 5:13 AM, zjxu wrote: > Jack Shultz 写道: > > The links to the videos don't work on this page. > Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video > 1,video 2,video 3) - (Gerrit Groenhof). > http://www.gromacs.org/Doc

Re: [gmx-users] trouble minimizing structure with mdrun

ugh it? > > Cheers, > > Tsjerk > > On Mon, Jan 4, 2010 at 1:38 AM, Jack Shultz > wrote: >> I've been having trouble minimizing a structure using gromacs so I >> decided to try using another MD app and see if I can generate a more >> relaxed structure. >&g

[gmx-users] trouble minimizing structure with mdrun

I've been having trouble minimizing a structure using gromacs so I decided to try using another MD app and see if I can generate a more relaxed structure. Using VMD & NAMD I was able to minimize and run MD for this structure from RCSB.ORG 1YQW.pdb. It was solvated and ionized. I then took the last

[gmx-users] Dead Link or Restricted Access to link

The links to the videos don't work on this page. Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video 1,video 2,video 3) - (Gerrit Groenhof). http://www.gromacs.org/Documentation/How-tos/QMMM -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing

Re: [gmx-users] tpr older version message

aminoacids.dat I downloaded it and everything seems to work. I will now make some additional steps on this workflow so this should now work! Thanks again for your help I very much appreciate it. On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> If I

Re: [gmx-users] tpr older version message

If I preped the tpr using amber forcefields, could that be the reason? The mdrun I am using does not have any force field libraries in its directory. On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> I preped this ligand using acpypi followed by grom

[gmx-users] tpr older version message

I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#m

Re: [gmx-users] Frequency confout is updated

I guess I misinterpreted the description. I take it there is no built in mechanism to periodically write the structure. Maybe I could revise the source code to write the structure at every checkpoint? On Wed, Dec 16, 2009 at 10:07 AM, Mark Abraham wrote: > Jack Shultz wrote: >> >>

[gmx-users] Frequency confout is updated

Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains

[gmx-users] combining minimization and md

I was wondering, is there a way you can prepare the parameter files so it will do a minimization followed by molecular dynamics? I think its a feature some other Molecular Dynamics apps support but I have not seen any example mdp files that describe this. -- Jack http://drugdiscoveryathome.com h

Re: [gmx-users] Grompp failed under double precision

value -2147483648. It should have been within [ 0 .. 1540 ] --- On Sun, Dec 6, 2009 at 7:43 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> We have a workflow going, and I switched to double precision because &

[gmx-users] Grompp failed under double precision

We have a workflow going, and I switched to double precision because of the LINCS issues. I got this error now with grompp. I don't think anything else is different other than double precision, but I included the logs for this. --- Program grompp

Re: [gmx-users] Reducing Standard Error output

>> >> Apparently this code is only used if the app is in verbose mode. So I >> guess we have two choices: >> 1) either find the cause of the lincs warnings > > That is always necessary if you don't want an expensive random number > generator. Your simulation system is ill conditioned, and the lincs

Re: [gmx-users] Reducing Standard Error output

e flag On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz wrote: > yes the environment I was running in was the boinc wrapper and its > supposed to somehow return the standard error output. It probably got > overloaded. It is curious why I only had the problem on windows 64 but > I'm no

Re: [gmx-users] Reducing Standard Error output

wrote: > Jack Shultz wrote: >> >> Thanks, >> >> I just figured out removing the -v will reduce output. Interestingly I >> only have this problem with 64-bit Windows hosts. I have not observed >> it in any others and I have a fairly diverse environment on this >&g

Re: [gmx-users] Reducing Standard Error output

ope it helps, > > Tsjerk > > On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz > wrote: >> Our first run typically produces this output >> >> Getting Loaded... >> Reading file md.tpr, VERSION 4.0.5 (single precision) >> Loaded with Money >> >>

[gmx-users] Reducing Standard Error output

Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime:95 s Fraction complete: 0.2 step 200, remaining runtim

Re: [gmx-users] Gromacs with QMMM Support

work is in Public Domain. On Mon, Nov 30, 2009 at 2:50 AM, wrote: > yes, that's right ;) > > > Quoting Jack Shultz : > >> I am reading this page >> http://wwwuser.gwdg.de/~ggroenh/qmmm.html >> >> Is it correct to assume you need one of the followin

[gmx-users] Gromacs with QMMM Support

I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list

Re: [gmx-users] Continue simulation

4, 2009 at 7:20 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> Is it ok just to use tpbconv, even though we get this message >> "Continuation should be done by loading a checkpoint file with mdrun >> -cpi"? >> > > Please

[gmx-users] Continue simulation

Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? ++ I have tried mdrun using the -cpi flag mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md Then when I run the next u

[gmx-users] User results for another run

I must have asked this before but I'm trying find the answer again. If I want to use the results from mdrun for another run following the first time interval, what do I need to do? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] Invoking parameters at startup

Ah yes thanks I came up with it after a little more testing. c:\ProgramData\BOINC\slots\4>echo LIG protein | g_rms.exe -s md.tpr -f md.xtc -n index.ndx -nice 19 On Fri, Nov 13, 2009 at 6:56 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> I am trying to sp

[gmx-users] Invoking parameters at startup

I am trying to specify protein and LIG as groups when I start certain analysis programs. I want to run this as part of a script. For example, if I want to run g_rms it will prompt me to specify the two groups we want to compare. I want to specify the groups when I start the app. Other than re-writi

[gmx-users] Generate an Index File

I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx -

Re: [gmx-users] How to generate xvg files

tcout = 10; Write coordinates to disk every nstxtcout steps Do I need to use this -x flag? mdrun -nice 0 -s em.tpr -x No xtc was created though On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey wrote: > > > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz > wrote: >> >

Re: [gmx-users] How to generate xvg files

calculates rmsd’s with a reference structure and rmsd matrices g rmsf calculates atomic fluctuations g energy writes energies to xvg files and displays averages On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey wrote: > > > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz > wrote: >> &g

[gmx-users] How to generate xvg files

Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: Remove solvent from results

I guess it can be done with sed but is there another way using one of the Gromacs apps? On Tue, Nov 10, 2009 at 12:48 PM, Jack Shultz wrote: > Hi Guys, > > I was wondering if there is any way to remove the solvent from your > final trajectory results in mdrun? > >

[gmx-users] Remove solvent from results

Hi Guys, I was wondering if there is any way to remove the solvent from your final trajectory results in mdrun? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Missing H from residue

Thanks Justin! Got it now. On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul wrote: >>> >>> Jack Shultz wrote: >>> >>> >>> >>>>

Re: [gmx-users] Missing H from residue

On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: > > > >> --- >> Program pdb2gmx, VERSION 4.0.5 >> Source code file: pdb2gmx.c, line: 429 >> >> Fatal error: >

Re: [gmx-users] Missing H from residue

M 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O On Mon, Nov 9, 2009 at 6:54 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> Well I was just wondering if there was some porgram that could add >> this atom automatically. It looks like this &q

Re: [gmx-users] Missing H from residue

cs/share/gromacs/top/ffamber99sb.rtp.bad- H amber99sb_17 0.29360 2 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-CA amber99sb_11 0.03970 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-HA amber99sb_19 0.11050 4 On Mon, Nov 9, 2009 at 4:26 PM, Mark Ab

[gmx-users] Missing H from residue

I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there

[gmx-users] Check out my photos on Facebook

invited to join Facebook by Jack Shultz. If you do not wish to receive this type of email from Facebook in the future, please click on the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955&u=10132975250&mid=145814aG5af318674a92G0G8 Facebook's offices are loca

Re: [gmx-users] Parameter to for randomizing simulation

, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> Hello, >> >> What parameter do I set in the mdp file to make it random every time it >> runs? >> > > Random starting velocities?  Use different values of gen_seed. > > -Justin >

[gmx-users] Parameter to for randomizing simulation

Hello, What parameter do I set in the mdp file to make it random every time it runs? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

Re: [gmx-users] Static build

Thanks, I switched to a fedora VM and it built properly. On Mon, Sep 28, 2009 at 4:26 AM, Ansgar Esztermann wrote: > > On Sep 27, 2009, at 6:24 , Jack Shultz wrote: > >> I'm trying to find a package that distributes libSM.a > > In case you have trouble finding the corr

Re: [gmx-users] Static build

I'm trying to find a package that distributes libSM.a On Sat, Sep 26, 2009 at 10:39 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> Hello, >> >> I am trying to build statically with the small source changes I made >> yesterday. >> >> I'm

[gmx-users] Static build

Hello, I am trying to build statically with the small source changes I made yesterday. I'm building on 32 bit linux with single precision. I have libSM [r...@vps gromacs-4.0.5]# ls /usr/lib/libSM* /usr/lib/libSM.so /usr/lib/libSM.so.6 /usr/lib/libSM.so.6.0.0 I get this error message cc -O3 -

Re: [gmx-users] timestep fraction complete

- f = fopen("progress.txt", "w"); src/mdlib/sim_util.c-125- if (!f) return; src/mdlib/sim_util.c-126- fprintf(f, "%g", (step - ir->init_step) / (float) ir->nsteps); src/mdlib/sim_util.c-127- fclose(f); src/mdlib/sim_util.c-128- } On Thu, Sep 24,

Re: [gmx-users] timestep fraction complete

Ah of course! fc = (int)dt / ir->nstlist; I should cast these as data types that support decimals right? On Thu, Sep 24, 2009 at 6:44 PM, Jack Shultz wrote: > I am hoping for an update every 10 minutes just to satisfy the anxieties of > volunteers crunching on my project, but every ho

Re: [gmx-users] timestep fraction complete

acked up md.edr to ./#md.edr.4# starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 100, remaining runtime: 122 s Fraction complete: 0 step 200, remaining runtime:92 s Fraction complete: 0 On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham wrote: > Jack Shul

[gmx-users] timestep fraction complete

I figured out another way to update the progress of my simulation, but I need to report the fraction of completion at the certain intervals of mdrun. Possibly at every time step or if that does not make sense every 100 timesteps. I don't think this is a feature currently supported, so I will have t

Re: [gmx-users] Consecutive Simulations

Thanks Justin, you are very helpful as always :-) On Thu, Sep 24, 2009 at 6:41 AM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: > >> If I run a simulation using mdrun and then run mdrun again, does it add >> another interval of simulation or does it just re-run the

[gmx-users] Consecutive Simulations

If I run a simulation using mdrun and then run mdrun again, does it add another interval of simulation or does it just re-run the last simulation. I'll elaborate so it makes a little more sense, our project has this progress bar that tells users the progress of the simulation. If I run mdrun for 10

Re: [gmx-users] Limit mdrun runtime

n. Note the use of exec instead of system exec "simulator --shell"; } } else { die "Could not fork."; } On Mon, Sep 14, 2009 at 11:56 AM, Jack Shultz wrote: > > So if I do this within a perl script, I will need to capture the pid and kill > that proces

Re: [gmx-users] Limit mdrun runtime

;t help. > You can kill mdrun using the kill command. > But since mdrun catches signals, you might need kill -9 (the 'KILL' > signal). > > Berk > > > Date: Mon, 14 Sep 2009 10:56:43 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subj

[gmx-users] Limit mdrun runtime

Hello, I have developed a workflow for prepping structures. One problem I have is sometimes it gets hung up on mdrun. Are there any mdrun parameters we can use to kill this process if it runs too long? The parameters we are using should not run over 5 minutes. I have not figured out how to do this

Re: [gmx-users] Re: Ligand & Receptor

This is neat! Thanks http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs On Fri, Jun 26, 2009 at 9:36 AM, Alan wrote: > Hi there, > How about taking a look at acpypi.googlecode.com and its wikis? > I hope it can help you. > Alan > On Fri, Jun 26, 2009 at 14:27, wrote: >> >> Hello, >> >> I

[gmx-users] Ligand & Receptor

Hello, I'm trying to figure out how I can merge the ligand and receptor files. I used this script to prep a ligand I treated with GAFF perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand This results in ligand.top & ligand.gro Then I prepped a receptor pdb2gmx_d -f fzd2.p

[gmx-users] Reducing Size of Data

Hi, I am taking a look at reducing the size of my analysis. I've decreased log writing intervals. I notice mdruns generate these pdb files. Is there any way of reducing the frequency these files are written? I think that will go a long way to making my analysis easier. 05/02/2009 07:34 PM

Re: [gmx-users] How to build a lipid bilayer in GROMACS?

I don't know if this helps you, but there is a membrane plugin for VMD which you can download for free. I've used this to insert proteins in membranes and then use namd to run MD. I don't know what steps are involved to make this structure compatible with GROMACS. http://www.ks.uiuc.edu/Research/v

[gmx-users] Missing atom in residue

Hi, What are some of the ways used to fix these problems? Do you manually manipulate these files to add missing residues or are there any automated methods? I tried ignoring it with -missing, which is probably a bad way to treat this error. Still that did not ignore the error. Does this require a

[gmx-users] Prepping Docking Complexes

Hi Guys, Thanks for previous help. Especially Justin. I got the amber03 and tip3 water models working through my BOINC project now. But if I want to simulate a docking complex, I'm running to some errors preparing it. I have not done extensive research on this yet, but I'm wondering how I can prep

[gmx-users] Water models for amber03

Hi all, I think I'm having a problem with the water models. Clearly ther are differences in these tip3p models. I can rename the ffamber_tip3p files to overwrite existing tip3p files. I don't want to do that because I want the option of choosing the amber ones at run-time. pdb2gmx does not accept

[gmx-users] Integrating with BOINC: failing at minimization

Hello, I've tried a couple ways of running the workshop tutorial with a different protein and amber03 force field. It works with a clean install of gromacs, but I am trying to integrate it into a grid computing project. https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf I tried s

[gmx-users] not referencing ffamber03.hdb

Hello, I have been trying to figure out why I'm getting this message. I looked over this site http://chemistry.csulb.edu/ffamber/index.html#usage But could not figure out why I'm getting this error. I'm running pdb2gmx_d.exe -ff amber03 WARNING: atom H is missing in residue LYSH 124 in the pdb

Re: [gmx-users] Range checking error: only on double precision

ou are running automated tests, since there are quirks > with requiring specific nomenclature (for lysine, histidine, terminal > residues, etc). > > -Justin > > Jack Shultz wrote: >> >> Justin, >> >> Can you suggest any pdb files I could use that are more simple

Re: [gmx-users] Range checking error: only on double precision

Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> Hello, >

[gmx-users] Range checking error: only on double precision

Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 --- Program mdrun, VERSI

[gmx-users] Reducing Size of Data

Hi, I was wondering if there are any ways to reduce the amount of data produce or compact it better. On some of my runs mdruns I ran out of the default disk space BOINC allocated for my file system to run this analysis. If I use the -compact flag, does that affect the size of the trajectory files?

[gmx-users] Re: Minimization not converging

eps, but did not reach the requested Fmax < 10. Potential Energy = -1.4354568e+06 Maximum force = 6.9535597e+10 on atom 25439 Norm of force = 4.5592896e+08 More details here. http://www.hydrogenathome.org/result.php?resultid=1291344 On Thu, Mar 12, 2009 at 10:59 AM, Jack Shultz wrote

[gmx-users] Minimization not converging

Hi, I think that my minimization are not running long enough. I've been following the parameters in tutorials but it seems like they all die at 34 steps I've been using these tutorials https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf http://md.chem.rug.nl/education/mdcourse/MDpr

Re: [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

ll it minimizes a system? On Wed, Mar 11, 2009 at 10:24 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> Has anyone come across this error on a windows platform? Any >> suggestions? I ran it through a BOINC workunit then tried it >> stand-alone for troubleshoot

[gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION

, pid 2396, thread main cs=001B ds=0023 es=0023 fs=003B gs= ss=0023 Stack trace: Frame Function Args 7FB40020 0044C09B (, , , ) End of stack trace On Wed, Mar 11, 2009 at 9:25 PM, Jack Shultz wrote: > Has anyone come across this error on a windows platf

[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316870 [main] mdrun 4084

Re: [gmx-users] redirect md.log to standard ourput

ok thanks, if it becomes critical to troubleshooting, I'll just get my hands dirty with the cpp code. On Wed, Mar 11, 2009 at 1:01 PM, Mark Abraham wrote: > Jack Shultz wrote: > >> I'm trying to capture errors when I run simulations through boinc. Is >> there a wa

[gmx-users] redirect md.log to standard ourput

I'm trying to capture errors when I run simulations through boinc. Is there a way to redirect the log to the standard output? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx

[gmx-users] Cuda support

Has anyone used these binaries? How are they? Any recommendations on using GPUs? https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gm

Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58

Oh I see this tutorial solvates before minimization. I'm heading out, but I'll give it a go tonight. On Mon, Mar 9, 2009 at 3:57 PM, Jack Shultz wrote: > Yes I read somewhere that treating the simulation space as a cube has > some drawbacks. I'll try these parameters. >

Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 58

Yes I read somewhere that treating the simulation space as a cube has some drawbacks. I'll try these parameters. On Mon, Mar 9, 2009 at 3:36 PM, Andrew Voronkov wrote: > I've used this tutorial: > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > > I've used command line:  edit

[gmx-users] visualizing trajectories real-time

I'm wondering if there are any GPL or GNU applications I can use to visualize simulations. I would like to integrate the code into a screen saver for my distributed computing project. -- Jack http://hydrogenathome.org ___ gmx-users mailing listgmx-

[gmx-users] Formating PDB Files

Hello, I am experimenting with formatting pdb files using pdb2gmx. Currently I am downloading ligand files from RCSB.ORG. These are non-protein pdb files. When I look at their residues, instead of having a standard residue, they use their pdb id as the residue id. pdb2gmx does not like this becaus

Re: [gmx-users] Support of Saddle Point Calculations

Thank you David, I am about halfway through the Gromacs 2007 Workshop material. Very nice. I'm wondering if there is any workshop videos covering QM/MM methods in Gromacs. Thanks, Jack On Sun, Oct 19, 2008 at 4:14 PM, David van der Spoel <[EMAIL PROTECTED]>wrote: > Jac

[gmx-users] Support of Saddle Point Calculations

Hello, I am fairly new to GROMACS but I have spent time running tutorials for several other molecular dynamics applications. I would like to know if the current framework for GROMACS has support for methods that calculate saddle point energy in first-order reactions. If so, are there examples I ca