Re: [gmx-users] Re: Job Crash

Yeah it was a permission error. It confused me because it happened mid stream. Sorry for wasting people time. ::) Thanks, Ilya On Mon, Mar 9, 2009 at 9:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Ilya Chorny wrote: I get the following and my job crashes. Is this just an i/o issue

[gmx-users] pdb2gmx -vsite h hangs

) There are 195892 donors and 195892 acceptors There are 280210 hydrogen bonds Checking for duplicate atoms Opening library file /data0/software/gromacs-4.0.4_cvs/share/top/specbond.dat 7 out of 7 lines of specbond.dat converted succesfully Thanks, Ilya -- Ilya Chorny Ph.D. -- Ilya Chorny Ph.D

Re: [gmx-users] pdb2gmx -vsite h hangs

/NH hydrogens. They don't describe using heavyh in the paper and there are earlier posts that teach away from using heavyh. Thanks, Ilya On Mon, Mar 9, 2009 at 7:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ilya Chorny wrote: Hi I am running 4.0.3. I wanted to test the 4fs timestep

[gmx-users] Infiniband Hardware

I am about to purchase some infiniband hardware and was wondering if anybody on the mailing list has experience/insight into what kinds of hardware to buy and what to stay away from. Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx

[gmx-users] Energy Drift in Gromacs 4.0

-warnangle = 30 ; Convert harmonic bonds to morse potentials morse= no -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: Energy Drift in Gromacs 4.0

-130.198-130198 On Tue, Mar 10, 2009 at 7:17 PM, Ilya Chorny icho...@gmail.com wrote: Hello All, I am trying to run some calibration calculations with 2/4 fs time steps. I am trying to reproduce the results in the Gromacs 4.0 paper on a protein/water (not the same protein) system with ~100K

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

be COM removal so I turned it off to no avail. Any chance one of the Gromacs people can give me the mdp file from the DHFR simulation in the 4.0 paper. On Tue, Mar 10, 2009 at 10:21 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Ilya Chorny wrote: Forgot column labels on energies

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

been minimized and has no major clashes. Thanks, Ilya On Wed, Mar 11, 2009 at 7:38 PM, Ilya Chorny icho...@gmail.com wrote: If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t

Re: [gmx-users] Height of the box

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/mailing_lists/users.php -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] pdb2gmx error

earlier post by Justin with a similar error message but no resolution. Anyone have anythoughts? Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] pdb2gmx error

On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following

Re: [gmx-users] pdb2gmx error

Thanks, this very helpful!!! Sent from my iPhone On Mar 15, 2009, at 3:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Tsjerk Wassenaar wrote: Hi, --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87

[gmx-users] Help parameterizing ddb to work with vsite -h option of pdb2gmx

between heavy atoms and not hydrogens. Why? Thanks, Ilya -- Ilya Chorny Ph.D. ___ 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

[gmx-users] Re: g_saltbr

. ARG24) and in others it list 1 charge group (i.e. ARG 36). Why is this? Thanks, Ilya -- Ilya Chorny Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

Re: [gmx-users] Re: g_saltbr

The code would not know that *a priori*. This list is generated before the frames are analyzed. Thanks, Ilya On Tue, Jul 27, 2010 at 12:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ilya Chorny wrote: I have a question about the g_saltbr output. I looked through the mailing list

Re: [gmx-users] Re: g_saltbr

...@vt.edu wrote: Ilya Chorny wrote: The code would not know that /a priori/. This list is generated before the frames are analyzed. I'm not implying that the code is going to pre-judge your system. If what you've shown is your output, wouldn't it make sense that g_saltbr only prints

[gmx-users] Re: Umbrella Sampling

-0.105314 9.004001-0.105302 9.006001-0.105293 -- Ilya Chorny Ph.D. ___ 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

[gmx-users] Re: Weird behavior with Pull code

that it jumps around at 1 ps intervals. If I set the value of nstxtcout to 1 then my output looks reasonable. Any ideas? Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] T-Coupling and COM removal

, lipid, and water and got a KE that was 1.5RT, 1.2RT, and .8RT respectively. My T is 298K. My COM removal and T-coupling is for the whole system. I am running 3.3.1. Is there a problem with T-coupling and COM removal on the whole system? Thanks, Ilya -- Ilya Chorny Ph.D

[gmx-users] Re: Strange PDO output during umbrella sampling

Scratch my post. I need to learn to read the manual more closely. I thought the PDO output was the distance and not the deviation from the restrained position. Thanks, Ilya On Sat, Feb 23, 2008 at 1:04 PM, Ilya Chorny [EMAIL PROTECTED] wrote: Hi All, I am trying to do umbrella sampling

[gmx-users] Strange PDO output during umbrella sampling

-- Ilya Chorny Ph.D. ___ 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

Re: [gmx-users] Merge two trajectories

/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 -- Ilya Chorny Ph.D

Re: [gmx-users] GROMACS vs NAMD

://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 -- Ilya Chorny Ph.D. ___ gmx-users mailing list

[gmx-users] How to center my trimer in my simulation box.

searched around for about an hour and could not find anything. I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. Any advice? Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

Re: [gmx-users] How to center my trimer in my simulation box.

Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL PROTECTED] wrote: Hello, I am

Re: [gmx-users] How to center my trimer in my simulation box.

Chorny [EMAIL PROTECTED] wrote: Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 22 Apr 2008 14:14:19 -0700 Ilya Chorny [EMAIL

Re: [gmx-users] How to center my trimer in my simulation box.

So I got it to work for my trimer by doing the following. 1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc 2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect The first step unwraps the whole trajectory and the second step wraps it back up. Cheers, Ilya -- Ilya Chorny Ph.D

[gmx-users] Re: Infiniband Setup Benchmark Results

through 64 and 87% @ 128. Not bad Cheers, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting