[gmx-users] Gromacs on GPU: GTX or Tesla?

Hi, We want to start using Gromacs on GPU and we are debating whether to purchase GeForce GTX card or Tesla platform. Looking at the published data it seems GTX580 has much impressive performance compared to Tesla C2050, and of course it is much cheaper. Is there a reason to prefer Tesla

[gmx-users] RE: Gromacs on GPU: GTX or Tesla?

Hi, In the long term the Tesla is much more preferable as the GTX would not support certain high end functions. Pls verify these before you purchase one. Also the Tesla C-2070 is the newer one available and with 6.0GB RAM it really gives out great performance. The price is the same. Rgds JSV

[gmx-users] Regarding Segmentation fault during mdrun_d

Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Cyclohexane box' 5 steps,100.0

Re: [gmx-users] Regarding Segmentation fault during mdrun_d

On Thu, Aug 4, 2011 at 3:03 PM, Ravi Kumar Venkatraman ravikumarvenkatra...@gmail.com wrote: Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads

Re: [gmx-users] Regarding Segmentation fault during mdrun_d

On 4/08/2011 5:03 PM, Ravi Kumar Venkatraman wrote: Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1

[gmx-users] g_dipoles - averaging

Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol'

[gmx-users] the density does not stablize

Dear gmxers, I try to perform NPT MD to obtain the density of system. But the value of density does not stablize even after over 40 ns. The content of mdp file can be seen below. How to deal with it? Please give me some hints. Thanks a lot for any replies. .mdp file: title

Re: [gmx-users] the density does not stablize

On 04/08/11, xiaowu759 xiaowu...@qq.com wrote: Dear gmxers, I try to perform NPT MD to obtain the density of system. But the value of density does not stablize even after over 40 ns. The content of mdp file can be seen below. How to deal with it? Please give me some hints. Thanks a lot

Re: [gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS

[gmx-users] g_membed stops after only one iteration

Hi I am trying to use g_membed to insert a protein into a bilayer. I made some changes to the sample.mdp file downloaded from the authors' homepage. The changes were: - reduced time step to 0.001 ps (instead of 0.002) - changed constraints to hbonds instead of all-bonds. g_membed runs fine, but

[gmx-users] Fwd: Regarding segmentation fault

 Please leave discussion on the mailing list so that the archives are available for posterity and that you might get input from more than one person. Apparently your .log file has been truncated abnormally, but the energy values reported are clearly indicative of

[gmx-users] Hydrogen atoms type

Hi Dear Users! I'm Using MMB to produce initial structures for my simulations. This program creating a .pdb file in output. The output file containing Hydrogen atoms that are not recognized by gromos53a5. I want to edit my pdb file but I can't find anything about hydrogen types in gromos! any

Re: [gmx-users] Hydrogen atoms type

Amir Abbasi wrote: Hi Dear Users! I'm Using MMB to produce initial structures for my simulations. This program creating a .pdb file in output. The output file containing Hydrogen atoms that are not recognized by gromos53a5. I want to edit my pdb file but I can't find anything about hydrogen

Re: [gmx-users] setting vdw cutoff with specific force-filed?

On 04/08/11, Justin A. Lemkul jalem...@vt.edu wrote: Yun Shi wrote: Hi all, I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a Lennard-Jones interaction function was used for short-range vdw interactions. From the reference paper /A Biomolecular Force Field Based on

[gmx-users] add Argon to a force field?

   Hi! I want to simulate an RNA molecule. I have the .pdb file of that. I want to create an Argon wall and make a hole on it to pull my molecule through it. Argon defined in OPLS/AA force field. but it has not nucleic acids. how can i define the argon in other force fields? -- gmx-users mailing

Re: [gmx-users] add Argon to a force field?

Amir Abbasi wrote: Hi! I want to simulate an RNA molecule. I have the .pdb file of that. I want to create an Argon wall and make a hole on it to pull my molecule through it. Argon defined in OPLS/AA force field. but it has not nucleic acids. how can i define the argon in other force

RE: [gmx-users] g_dipoles - averaging

Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg

[gmx-users] PRODRG topology

Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4

Re: [gmx-users] PRODRG topology

Marzinek, Jan wrote: Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb

Re: [gmx-users] setting vdw cutoff with specific force-filed?

Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong here? I understand

Re: [gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van der Waals Parameters) to calculate non-bonded vdw interactions that are not between third neighbors, such as CH1 carbons between different chains in a biomolecular system. Anything wrong

RE: [gmx-users] g_dipoles - averaging

On Thu, 2011-08-04 at 15:49 +0100, Kukol, Andreas wrote: Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: To obtain the

Re: [gmx-users] RE: Gromacs on GPU: GTX or Tesla?

Hi, Tesla cards won't give you much benefit when it comes to running the current Gromacs. Additionally, I can tell you so much that this won't change in the future either. The only advantage of the C20x0-s is ECC and double precision - which is ATM anyway not supported in Gromacs on GPUs.

[gmx-users] angular velocities in gromacs?

Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Thanks for the information! Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Re: setting vdw cutoff with specific force-filed?

Hi Justin, I got it now. During the 10fs, even water molecules with a speed of 500 m/s only have a 0.005 nm displacement, which is far less than than 0.9 nm or 1.4 nm. Thanks again! Yun Yun Shi wrote: Hi Justin and Mark, Thank you very much for the reply. I was using table 7 (Normal van

Re: [gmx-users] Problem of Kinetic Energy

On 4/08/2011 7:17 AM, Size Zheng wrote: Hi Mark, When I used the g_traj with options of -ekt and -ekr, i made a selection as follow Group 0 ( System) has 6400 elements Group 1 (TP4) has 6400 elements Select a group: 1 Selected 1: 'TP4' So according to you that

Re: [gmx-users] angular velocities in gromacs?

On 5/08/2011 6:08 AM, Tom wrote: Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Angular velocities with respect to what? Mark -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?

Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus’s group (J. Am. Chem. Soc. (1990) 112, 9161-9175. J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions)

Re: [gmx-users] angular velocities in gromacs?

Hi Tom, TRR files contain velocities for individual atoms as a function of time, which is all the velocity information there is in an MD simulation. You can reduce that information to rotation about a principle molecular axis, or rotation with respect to the simulation box, or whatever you need.

Re: [gmx-users] How to exclude the interactions between molecule A and B in Gromacs?

On 5/08/2011 1:17 PM, DeChang Li wrote: Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus's group (J. Am. Chem. Soc. (1990) 112, 9161-9175. J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the