[gmx-users] Re: g_velacc

I have taken the fit for 2ns in Einsteins curve to calculate the diffusion coefficient but when i take the values up to 100 ps for velocity auto correlation i get the matching result...Is it good to do such thing? i will be happy if you guide me. I have attached the graph of VAC herewith. Thanks

Re: [gmx-users] Re: g_velacc

On 2013-07-05 10:50, Ishwor wrote: I have taken the fit for 2ns in Einsteins curve to calculate the diffusion coefficient but when i take the values up to 100 ps for velocity auto correlation i get the matching result...Is it good to do such thing? i will be happy if you guide me. I have attached

[gmx-users] Inconsistent results between 3.3.3 and 4.6 with various set-up options

Hi everyone, I have been doing some tests and benchmarks of Gromacs 4.6 on a GPU cluster node (with and without GPU) with a 128 lipid bilayer (G53A6L FF) in explicit solvent and comparing it to previous results from 3.3.3. Firstly I wanted to check if the reported reaction field issues of 4.

[gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

Sorry, the tables got all messed up. I've converted them to just text now: From: cara_...@hotmail.com To: gmx-users@gromacs.org Subject: Inconsistent results between 3.3.3 and 4.6 with various set-up options Date: Fri, 5 Jul 2013 17:31:04 +0800 Hi everyone, I have been doing some tests and

Re: [gmx-users] Re: g_velacc

Use this command line: -- g_velacc -nonormalize -acflen 2001 -- g_integrate -f vac.xvg -integrate -- Multiply the resulting value by 333.333, the result will be self-diffusion coefficient expressed as result * 10^(-9) m^2/s. The velocities should be written down at least every 10fs during MD. The

Re: [gmx-users] Re: g_velacc

"g_integrate" should be "g_analyze" below. Sorry. On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban wrote: > Use this command line: > > -- g_velacc -nonormalize -acflen 2001 > -- g_integrate -f vac.xvg -integrate > -- Multiply the resulting value by 333.333, the result will be > self-diffusion

Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

On 2013-07-05 11:52, Cara Kreck wrote: Sorry, the tables got all messed up. I've converted them to just text now: From: cara_...@hotmail.com To: gmx-users@gromacs.org Subject: Inconsistent results between 3.3.3 and 4.6 with various set-up options Date: Fri, 5 Jul 2013 17:31:04 +0800 Hi ev

Re: [gmx-users] shell MD

In which case can the determinant not be computed? Dr. Vitaly V. Chaban On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote: > Dear users, > > I'm trying to run MD with SWM4-DP model (data from > http://virtualchemistry.org), but I always have error: > "Can not invert matrix, determinant =". > > I

Re: [gmx-users] shell MD

In case of MD run. Minimization procedure was successful. 05.07.2013, 14:48, "Dr. Vitaly Chaban" : > In which case can the determinant not be computed? > > Dr. Vitaly V. Chaban > > On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote: > >>  Dear users, >> >>  I'm trying to run MD with SWM4-DP model (dat

RE: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

> Date: Fri, 5 Jul 2013 12:38:15 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with > various set-up options > > On 2013-07-05 11:52, Cara Kreck wrote: > > Sorry, the tables got all messed up. I've convert

Re: [gmx-users] shell MD

The was a bug report on this error a few years ago, http://redmine.gromacs.org/issues/332 Can your problem correlate with that discussion, perhaps? Dr. Vitaly V. Chaban On Fri, Jul 5, 2013 at 1:58 PM, Sergey wrote: > In case of MD run. Minimization procedure was successful. > > 05.07.2013,

Re: [gmx-users] shell MD

Possibly, can :) I will have to run shell MD in NAMD, though it will be slower a bit. Seemingly, only Vitaly see my problem :). 05.07.2013, 16:31, "Dr. Vitaly Chaban" : > The was a bug report on this error a few years ago, > http://redmine.gromacs.org/issues/332 > > Can your problem correlate wit

Re: [gmx-users] shell MD

Vitaly saw this problem while running gromacs/mopac interface about 4 years ago... The impression was that the problem is related to incorrectly computed forces. I would file a bug report. Dr. Vitaly V. Chaban On Fri, Jul 5, 2013 at 2:43 PM, Sergey wrote: > Possibly, can :) > I will have t

[gmx-users] Increase in kinetic energy in LINCS with smaller time step

Dear Gromacs users, I have a question about an effect of time-step on results of simulation with LINCS. Now, I am running on a MD simulation of a rigid molecule in vacuum under NVE ensemble. No temperature coupling was used. No inter-atomic potential was used. The rigid molecule is consisting of

[gmx-users] Increase in kinetic energy in LINCS with smaller time step

Dear Gromacs users, I have a question about an effect of time-step on results of simulation with LINCS. Now, I am running on a MD simulation of a rigid molecule in vacuum under NVE ensemble. No temperature coupling was used. No inter-atomic potential was used. The rigid molecule is consisting of

[gmx-users] Larger number of decimal places for coordinates with velocities

Dear all, I use Gromacs 4.5.5 with the AMBER ff99SB force field. I'm working on a method that requires me to run short NVE simulations one after the other, but randomly generating velocities at the start of each simulation. i.e. I would run 10 ps, use the final structure with new random velocitie

[gmx-users] GROMACS 4.6.3 released

Hi GROMACS users, GROMACS 4.6.3 is officially released. It contains one major bug fix; a significant simulation performance regression with MPI-enabled builds was introduced in 4.6.2. Several less critical issues have also been addressed. We encourage all users to upgrade their installations from

[gmx-users] charmm2gromacs-pvm.py error

Hlello: I am trying to run charmm2gromacs-pvm.py with command: charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf but it failed with messages: Creating cgenff-2b7.ff files... Traceback (most recent call last): File "charmm2gromacs-pvm.py", line 283, in name = segments[1]

[gmx-users] Re: Re: unwrap trajectory file using -pbc nojump

Hi Tsjerk, Thanks for helping me. I can run trjconv without nojump. And when I use gmxcheck, it gives the following output: Warning at frame 5: coordinates for atom 7035 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06) Warning at frame 5: coordina

[gmx-users] transfering files from host computer to lyceum

Hi, I am a new user to linux, lyceum and gromacs. I was just wondering if anyone knew what exactly to do to transfer files from the host computer to lyceum? I really need help. Thanks in advance, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/transfering-files-from

Re: [gmx-users] Inconsistent results between 3.3.3 and 4.6 with various set-up options

On Fri, Jul 5, 2013 at 11:31 AM, Cara Kreck wrote: > > > > Hi everyone, > > I have been doing some tests and benchmarks of Gromacs 4.6 on a GPU cluster > node (with and without GPU) with a 128 lipid bilayer (G53A6L FF) in explicit > solvent and comparing it to previous results from 3.3.3. Firstl

Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

On Fri, Jul 5, 2013 at 11:52 AM, Cara Kreck wrote: > Sorry, the tables got all messed up. I've converted them to just text now: > > From: cara_...@hotmail.com > To: gmx-users@gromacs.org > Subject: Inconsistent results between 3.3.3 and 4.6 with various set-up > options > Date: Fri, 5 Jul 2013 17

Re: [gmx-users] Larger number of decimal places for coordinates with velocities

On Fri, Jul 5, 2013 at 5:16 PM, C.M.Sampson wrote: > Dear all, > > I use Gromacs 4.5.5 with the AMBER ff99SB force field. > > I'm working on a method that requires me to run short NVE simulations > one after the other, but randomly generating velocities at the start of > each simulation. i.e. I wo

Re: [gmx-users] transfering files from host computer to lyceum

On 7/5/13 1:24 PM, chinnu657 wrote: Hi, I am a new user to linux, lyceum and gromacs. I was just wondering if anyone knew what exactly to do to transfer files from the host computer to lyceum? Any basic Linux tutorial or textbook will discuss sftp, scp, etc. There are other forums for Lin

Re: [gmx-users] Larger number of decimal places for coordinates with velocities

Have you checked out the -ndec option for trjconv? If you have a high precision format (.trr, or .xtc if they are stored with sufficient precision) you can print out a .gro file (that gromacs can read) with higher precision. Gromacs can read .gro files with increased precisions in the coordinates

[gmx-users] about adding forcefield in the list of pdb2gmx

Hi all GROMACS users I added a new forcefield  folder to head node in /opt/bio/gromacs/share/gromacs/top  and it appears in the list of forcefield in pdb2gmx while I run it from head node of cluster. But if I run pdb2gmx from other slave nodes , it do not appear in the list. So, Please could

[gmx-users] 11-cis retinal topology problem

Hello guys: I am building 11-cis-retinal topology these days. Here is what I did: first of all, I build a small peptide like compound which contains:11-cis-retinal connected to the protonated sidechain of LYS, ACE and NME capped the N-term and C-term of the LYS respectively. With this compo