Re: [gmx-users] Gromacs 4.5.5

On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina" wrote: > > Dear All, > > I've had to re-install my gromacs on my computer and I'm having issues getting past the "Making all in Man7" during the "make" stage. There is no error in the output you show. Grepping for "error" doesn't really help when there

Re: [gmx-users] Re: NVT .gro for NPT

On Mon, Jun 17, 2013 at 8:12 AM, maggin wrote: > Hi, Tsjerk > > You asked me a good question. > > Ya, sometime it accords my imagination to tell if it right or not. That's > not the correct way. > > Maybe it near boundary, like at the boundary of dangerous. So let me have > such question. > Whe

Re: [gmx-users] Re: Gromacs 4.5.5

Hello Maggin, I re-installed both cmake and fftw. Now I no longer have an output from "grep -i error make. log". However I still can't get past the same stage in "Making all in man 7". Sent from my Ultrafast Samsung Galaxy S4 on Three Original message From: maggin Date: 1

Re: [gmx-users] Gromacs 4.5.5

Thank you Mark. Sent from my Ultrafast Samsung Galaxy S4 on Three Original message From: Mark Abraham Date: 17/06/2013 08:02 (GMT+00:00) To: Discussion list for GROMACS users Subject: Re: [gmx-users] Gromacs 4.5.5 On Jun 16, 2013 7:58 PM, "Emmanuel, Alaina" wrote: > > De

Re: [gmx-users] Re: Gromacs 4.5.5

Thank you very much for your help Mark and Maggin :) (Please ignore my last message to you, Maggin.) Sent from my Ultrafast Samsung Galaxy S4 on Three Original message From: "Emmanuel, Alaina" Date: 17/06/2013 10:48 (GMT+00:00) To: Discussion list for GROMACS users Subjec

[gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

Dear GROMACS list, I used minVar to remove global rotations and translations from a trajectory, but due to memory issues I used a replica with only the backbone of the protein. Now I want to fit each frame of the original protein trajectory to the respective frame of the processed backbone traject

[gmx-users] Re: QM/MM simulations

Hello, Justin. I try to find information about it, but all examples is old and there is nothing about it in new manuals. I will be very grateful if you describe me a procedure of connecting orca library to mdrun. David -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-

Re: [gmx-users] autocorrelation output g_hbond

Hi, Yes, the forward and backward rate constants are for hydrogen-bond breaking and reforming. You seem to have too poor statistics to draw conclusions about the backward rate, however. You probably need to simulate longer. Erik On 15 Jun 2013, at 00:38, learnmd wrote: > Hi, > > I have run

[gmx-users] gromos force field in PRODRG server

Dear gromacs users I want to do MD simualation for a protein-ligand system. For ligand, I use PRODRG server. I know that this server generate a *.itp file for ligand based on gromos force field. There are 5 versions for gromos force field (GROMOS96 43a1, GROMOS96 43a2, GROMOS96 45a3, GROMOS96 5

Re: [gmx-users] autocorrelation output g_hbond

…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler model for whatever reason. Erik On 17 Jun 2013, at 13:22, Erik Marklund wrote: > Hi, > > Yes, the forward and backward rate constants are for hydrogen-bond breaking > and reforming. You seem to have too poor statist

[gmx-users] list of missing LJ-14 interactions:

Dear gmx users, I have simulated the heme protein using gromos43a5 ff. I have used virtual sites2 for the CO ligand and it successfully runs without any error upto equilibrium state ( em, nvt and npt). However,when i start running production for 10 ns and it stopped step 17400 and shows few

[gmx-users] How to check if one protein broke into fragments during MD?

Hi, all 1dx0.pdb during MD step at 19532ps are broken into 8 fragments, as VMD show about bovin19532.gro as picture shows that at the bottom the number of protein is 8 while when I use VMD to see md_0_1.gro the last structure of MD f

Re: [gmx-users] Re: QM/MM simulations

On 6/17/13 7:16 AM, DavidPO wrote: Hello, Justin. I try to find information about it, but all examples is old and there is nothing about it in new manuals. I will be very grateful if you describe me a procedure of connecting orca library to mdrun. At this point, you don't need a tutorial or

Re: [gmx-users] gromos force field in PRODRG server

On 6/17/13 9:17 AM, shahab shariati wrote: Dear gromacs users I want to do MD simualation for a protein-ligand system. For ligand, I use PRODRG server. I know that this server generate a *.itp file for ligand based on gromos force field. There are 5 versions for gromos force field (GROMOS96

Re: [gmx-users] How to check if one protein broke into fragments during MD?

On 6/17/13 11:00 AM, maggin wrote: Hi, all 1dx0.pdb during MD step at 19532ps are broken into 8 fragments, as VMD show about bovin19532.gro as picture shows that at the bottom the number of protein is 8 while when I use VMD to se

Re: [gmx-users] list of missing LJ-14 interactions:

On 6/17/13 10:15 AM, 라지브간디 wrote: Dear gmx users, I have simulated the heme protein using gromos43a5 ff. I have used virtual sites2 for the CO ligand and it successfully runs without any error upto equilibrium state ( em, nvt and npt). However,when i start running production for 10 ns and

[gmx-users] CUDA with QUADRO GPUs?

Dear all, I am considering buying a workstation with a Quadro K2000 or K4000 GPU. According to this NVIDIA site these GPU have more "compute capability" than most of the Tesla cards (except for the K20): https://developer.nvidia.com/cuda-gpus In particular, much more "compute capability" than th

[gmx-users] RE: Re: RE: Re: RE: About the binary identical results by restarting from the checkpoint file

Hi Mark, I test the simulations again using Berendsen thermostat in Gromacs Version 4.6.2. Below are the procedures and results: 1. Gromacs version 4.6.2 (gromacs462_openmp_mkl_nogpu): Run simulation NO. 1: mdrun -v -nt 1 -ntmpi 1 -cpt 0 -s md.tpr -nsteps 1000 -deffnm md -reprod and: mdrun

Re: [gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

Hey Thomas, No, there is no such tool. Sorry. May I ask how you did the MinVar fitting? Cheers, Tsjerk On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis wrote: > Dear GROMACS list, > > I used minVar to remove global rotations and translations from a > trajectory, but due to memory issues

[gmx-users] Re: MD run - gen_vel

On 6/17/13 4:13 PM, Dariush Mohammadyani wrote: Dear Justin, I have sent a post on GROMACS-user and did not get any answer. Could you please help me out to find the answer? I did not see the original post, but that doesn't really matter. Please keep all Gromacs-related questions on the gm

[gmx-users] question regarding mutation from CH --> COH during free energy calculation

Hi, I sent the following email last Saturday and I haven't got any reply yet. I wonder whether you can suggest something regarding this issue. Thanks in advance. ** I edit my topology file for mutating CH --> C

Re: [gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

Hi Tsjerk, Here's the command line: minVar -s backbone.pdb -f backbone.xtc -log minVar_method3 -out backbone_minVar+NN.xtc -method 3 -NN 80 -nt_iter 8 -nt 8 -cycle_num 100 -mwa Thomas On 17 June 2013 23:37, Tsjerk Wassenaar wrote: > Hey Thomas, > > No, there is no such tool. Sorry. > May I

Re: [gmx-users] CUDA with QUADRO GPUs?

Dear Ramon, Compute capability does not reflect the performance of a card, but it is an indicator of what functionalities does the GPU provide - more like a generation number or feature set version. Quadro cards are typically quite close in performance/$ to Teslas with roughly 5-8x *lower* "GROMA

[gmx-users] Re: How to check if one protein broke into fragments during MD?

Hi, Justin the structure of 19532ps shows as the structure of md_0_1 shows as So, how can I fix the structure of 19532ps like md_0_1 ? Thank you very much! maggin -- View

Re: [gmx-users] Re: How to check if one protein broke into fragments during MD?

On 6/17/13 9:59 PM, maggin wrote: Hi, Justin the structure of 19532ps shows as the structure of md_0_1 shows as So, how can I fix the structure of 19532ps like md_0_1 ? As I

[gmx-users] grompp error

Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, plea

[gmx-users] Re: How to check if one protein broke into fragments during MD?

Hi, Justin, use: trjconv -dump 19532 -pbc nojump -s md_0_1.tpr -f md_0_1.xtc get: Thank you veru much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-check-if-one-protein-broke-into-fragments-