[gmx-users] Re: gmx in GPU calculation

Dear all: I am troubled with this problem: when I run mdrun_openmm fias in GPU calculation of gmx, I met the following information: Back Off! I just backed up md.log to md.log.2 Getting Loaded... Reading file 1.tpr, VERSION 4.0.3 (single precision) Note: tpx file_version 58, software version 59 S

[gmx-users] gmx in GPU calculation

generally, try to reduce the problem to something simpler. Therefore try the *exact* same thing on a non-gpu run. That said, it seems pretty clear that you created a .tpr file with a higher version of grompp and then tried to run it with a lower version of mdrun... or something like that, b

[gmx-users] gmx in GPU calculation

Dear all: I am troubled with this problem: when I run mdrun_openm faaia in GPU calculation of gmx, I met the following information: *Back Off! I just backed up md.log to md.log.2* ** *Getting Loaded...* ** *Reading file 1.tpr, VERSION 4.0.3 (single precision)* ** *Note: tpx file_version 58, soft

[gmx-users] Fwd: Force Field - Gromos96

-- Forwarded message -- From: tree Date: Thu, Mar 12, 2009 at 10:09 PM Subject: Force Field - Gromos96 To: gmx-users@gromacs.org Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 forc

[gmx-users] free energy coupling/decoupling equivalence

Hello, I have just read an interesting paper suggesting that the reference state in free energy decoupling/coupling simulations should be the one with larger entropy. Lu and Kofke "Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling" JCP V. 114, N. 17 pp. 7303-7

[gmx-users] Force Field - Gromos96

Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim __

[gmx-users] problems with gmxtest.pl

Dear users and developers of gromacs, despite checking for the usage of the proper version of tests after upgrading to gromacs-4.0.4 the test suite still produces results with the status FAILED. This is the case for some tests in kernel, complex, and pdb2gmx. For example kernel020 fails with /kern

Re: [gmx-users] about the restart of the mdrun

sheerychen wrote: Hello, I have a problem when I restrat of mdrun (Gromacs 4.0) using the following command: mdrun -deffnm Asp -cpi -append. The errors like this: eading checkpoint file Asp_md.cpt generated: Wed Mar 11 19:16:24 2009 Build time mismatch, current program: Thu Mar 5 17:52

Re: [gmx-users] removal of COM

Sun Joo Lee wrote: Hello Users I am trying to measure the drift of molecules in the system. When I ran the simulation, the removal of center-of-mass of the whole system took place at every step. From the mailing list, I've found that removal of COM works by making the velocity of the COM t

Re: [gmx-users] Reducing Size of Data

Jack Shultz wrote: 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

Re: [gmx-users] Reducing Size of Data

Jack Shultz wrote: 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 o

[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?

Re: [gmx-users] problem in energy minimization

Abhik Mukhopadhyay wrote: Hi everyone, I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization

[gmx-users] removal of COM

Hello Users I am trying to measure the drift of molecules in the system. When I ran the simulation, the removal of center-of-mass of the whole system took place at every step. From the mailing list, I've found that removal of COM works by making the velocity of the COM to be zero by subtra

[gmx-users] problem in energy minimization

Hi everyone, I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization with all-bonds constraint, bu

Re: [gmx-users] Variance in ED

Hi Andrea, The variance associated with an eigenvector is the eigenvalue. The sum of the eigenvalues captures the total variance. Accordingly, dividing an eigenvalue by the sum of all eigenvalues gives the part of the total variance explained by the eigenvector. Cheers, Tsjerk On Thu, Mar 12, 2

Re: [gmx-users] pdb files

oguz gurbulak wrote: Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Read the manual, section 5.6.1. -Justin

[gmx-users] problems with gmxtest.pl

Dear users and developers of gromacs, although running the tests is straight forward some advice how to interpret the results would be helpful. If a test ends with Testing xyz . . . PASSED but check mdp file differences and 'diff' of the mdp files shows a differenet file header only everything see

Re: [gmx-users] pdb files

Will I write two  .rtp files for two different molecules ? or Will I write  one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top )  ? Thanks in advance --- On Thu, 3/12/09, Justin A. Lemkul wrote: From

[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials

Hello again. It's pretty clear now for me thanks. I still have a little problem due to the unphysical trend of the BKS potentials for r --> 0 : it goes to minus infinity. The atoms can thus collide in case of a high temperature (providing them enough velocity to overcome the barrier) and I get the

Re: [gmx-users] pdb files

Justin A. Lemkul wrote: oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA

Re: [gmx-users] pdb files

oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either

[gmx-users] Variance in ED

Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- Andrea Carotti Dipartimento di Chim

Re: [gmx-users] pdb files

Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? Thanks in advance < wrote: From: Justin A

Re: [gmx-users] Re: Minimization not converging

Jack Shultz wrote: I should have included some output Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439 Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439 Stepsize too small, or no change in energy. Converged to machine precision, but

[gmx-users] Re: Minimization not converging

I should have included some output Step= 32, Dmax= 2.4e-06 nm, Epot= -1.03223e+05 Fmax= 3.87326e+06, atom= 25439 Step= 33, Dmax= 1.2e-06 nm, Epot= -1.03222e+05 Fmax= 3.87334e+06, atom= 25439 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested pr

[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] How to carry out rigid body

In the case of Martini(CG)-derived protein simulations we use an elastic network to connect the backbone (C-alpha) beads. This allows to control the conformation and dynamics of the protein. We parameterized this EN to reproduce atomistic simulations and observed that with a cutoff of 0.8

[gmx-users] How to carry out rigid body

Hi everyone, I want to peform CG-MDs with gromacs. In my system, there are some rigid bodies which are composed by hundreds of LJ atoms. Atoms of each rigid body move together in LJ water solution. How can I deal with it? Any suggestion is appreciated. Thanks in advance. -- wende

RE: [gmx-users] viscosity calculation using g_energy (3.3.3)

Hi, This is a very inefficient method for determining the viscosity. Also you need really perfect pressure fluctuations: NVT, shifted potentials, probably even double precision. There was a mail about this recently. There are better methods, have a look at: http://dx.doi.org/10.1063/1.1421362

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

Hi, Everything depends completely on how much drift you are talking about. There will always be energy drift, it is just a question how much. In general shifted potentials will be cheaper (and lead to less energy drift) than setting nstlist to 1, but for most purposes a bit of energy drift is no

Re: [gmx-users] Karplus parameterization

XAvier Periole wrote: Dears, Anyone knows which parameterization of the Karplus equation is implemented in g_chi ? Hm, I'm surprised to see this isn't in the source code with a please_cite call. My bad, this is at least one of them. @Article{ Vuister93, author = "G. W. Vuister and

[gmx-users] Karplus parameterization

Dears, Anyone knows which parameterization of the Karplus equation is implemented in g_chi ? Best, XAvier. XAvier Periole MD-group University of Groningen The Netherlands ___ gmx-users mailing listgmx-users@gromacs.or

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

Even if a system is not well equilibrated (but not so far from equilibrium) ,energy should be conserved in NVE ensemble. Try to lower the nstlist from 10 to 1 i.e. renew every time the neighbourlist. In systems I have studied, that is the key that improve much more energy conservation. It works

[gmx-users] about the restart of the mdrun

Hello, I have a problem when I restrat of mdrun (Gromacs 4.0) using the following command: mdrun -deffnm Asp -cpi -append. The errors like this: eading checkpoint file Asp_md.cpt generated: Wed Mar 11 19:16:24 2009 Build time mismatch, current program: Thu Mar 5 17:52:53 CET 2009 chec

Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

David, Thanks for the quick reply. Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg The output file created includes three columns. 1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). The b

Re: [gmx-users] Broken trr-file

Mark Abraham wrote: Justin A. Lemkul wrote: Hansjoerg Jerabek wrote: Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Readin