Re: [gmx-users] Error: Not enough ref_t and tau_t values

Thank you Tsjerk;   I followed your advice, and it looks working well.   Cheers,   Hiromichi - Original Message - From: Tsjerk Wassenaar To: Discussion list for GROMACS users Sent: Wednesday, June 14, 2006 8:13 PM Subject: Re: [gmx-users] Error: Not enough r

[gmx-users] GROMACS SGI Error

Hi   I am trying to install GROMACS 3.3.1 on SGI Irix 6.5.20m.   I installed and used fftw-3.1.1 during the compiling of gromacs.   After I configure using   ./configure –prefix=/usr/people/guest/gromacs   I did   make   and got the following error _

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Hi Francisco, was wondering if you ever resolved this issue? I too am trying to install gromacs mpi on our cluster, but have had no luck. I get the following error in the configure step: [EMAIL PROTECTED] gromacs-3.3.1]$ ./configure --enable-mpi --prefix=/home/ababakha/gromacs-3.3.1 checkin

[gmx-users] g_hbond -hx bug ?

Dear all, I have a problem with the option -hx of g_hbond in the 3.3.99_development_20060306 version of GROMACS. Indeed I have a 75-residue long helicoidal protein, and I expected to obtain between 40 and 50 hbonds between residues n,n+4. But g_hbond gave me about 10 (n,n+4) hbonds, whereas more

Re: [gmx-users] quality of cluster strucutres

Mauricio Sica wrote: Dear all I´ve obtained one cluster structure from a protein simulation. Then, as I wanted to use this structure as a static model, I checked it with WHAT_IF and the result was that as a model is a little poor (a list of bad angles, bad distances, problems with planarity and

[gmx-users] quality of cluster strucutres

Dear all I´ve obtained one cluster structure from a protein simulation. Then, as I wanted to use this structure as a static model, I checked it with WHAT_IF and the result was that as a model is a little poor (a list of bad angles, bad distances, problems with planarity and so on as you can imagin

Re: [gmx-users] diffusivity computations

Debashis Dutta wrote: Hi all, I have been trying to estimate the diffusivity of an alanine molecule in water with the .mdp file (for md simualtions) given below. When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreo

Re: [gmx-users] GROMACS in parallel

Akshay Patny wrote: Dear Sir I am trying to install GROMACS. I have tried to install program and it goes through okay. However, when I try to compile the program in parallel using the –enable-mpi option, it gives me an error: “Cannot compile and link MPI code with cc” See below for t

[gmx-users] GROMACS in parallel

Dear Sir   I am trying to install GROMACS. I have tried to install program and it goes through okay. However, when I try to compile the program in parallel using the –enable-mpi option, it gives me an error: “Cannot compile and link MPI code with cc”   See below for the command and the

[gmx-users] diffusivity computations

Hi all, I have been trying to estimate the diffusivity of an alanine molecule in water with the .mdp file (for md simualtions) given below. When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreover, the estimated dif

Re: [gmx-users] gromacs parallel doesn't work

Ok, got it to work. (I had to go back and reinstall the parallel version of mdrun). question though: I notice that there's a log file created for each node (so in my case, there are 4 log files). Why is this, is this typical? I guess what I'm asking is, how exactly does GROMACS divide the p

Re: [gmx-users] mdrun error with QM/MM with Gromacs-CPMD

Hi Maham, You need to edit the script 'cpmdmpi' so that it does have the path to access the cpmd.x from your working folder. The error message is due to that; it is not being able to access cpmd.x. 1. If you are using a serial version of CPMD then create a script 'cpmdmpi' with the following line

Re: [gmx-users] termini database

Debashis Dutta wrote: Hi all, can anyone tell me the command to generate a chain of amino acids using the exisiting database in gromacs? Also, how can we add the terminal NH3+ and COO- groups using the termini database. please make your question more clear. do you want to generate co

[gmx-users] termini database

Hi all, can anyone tell me the command to generate a chain of amino acids using the exisiting database in gromacs? Also, how can we add the terminal NH3+ and COO- groups using the termini database. Thanks Debashis _

[gmx-users] mdrun error

In God We Trust Hello Dr Biswas Yes, our  run created  the output.pdb2gmx, output.grompp_em and output.mdrun_em. Output.pdb2gmx and output.grompp_em  haven't any error message but output.mdrun_em has an error .I attached it to this mail.  Thank you very much in advance for your kindness and yo

Re: [gmx-users] Need topology for selenomethionine

Sridhar Acharya wrote: Hi all, Has anybody built a gromax topology for selenomethionine? How the topology can be incorporated into the existing gromacs topology files? It might exist on the website. You just need to replace the sulphur by Se, probably with a slightly larger sigma. Check liter

[gmx-users] Need topology for selenomethionine

Hi all, Has anybody built a gromax topology for selenomethionine? How the topology can be incorporated into the existing gromacs topology files? thanks in advance. sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http:

Re: [gmx-users] Error: Not enough ref_t and tau_t values

Hi Hiromichi,It is likely that you have some groups which are not covered by "Protein" and "Other". You can use "Protein" and "Non-Protein" in stead. But make sure that the two groups correspond to two distinct groups in your system. You may run into trouble if you have some non-standard residue in

[gmx-users] Error: Not enough ref_t and tau_t values

Dear all;   I am trying to calculate the binding free energy of an MHC-molecule and a peptide by thermodynamic integration method. The system contains binding domain of MHC molecule, a peptide presented on it, water-molecules (about 13,000), and ions (Na+ and Cl- at PBS-concentration). Afte

[gmx-users] Wrong Diffusion/Compressibility for Coarse-grained Water

Dear all, I am trying to get my feet wet with the Coarse-grained Force Field developed by Marrink et al. I've downloaded the examples of top-File, gro-file and mdp-file for the Water model on Marrink's website. Unfortunately, I didn't succeed to reproduce the diffusion constant and isothermal co

Re: [gmx-users] gromacs parallel doesn't work

Arneh Babakhani wrote: grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o ResMD1 ; you need -np 4 for grompp mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g ResMD1 > & ResMD1.job & Mark Abraham wrote: Arneh Babakhani wrote: Hello, I'm having a s

Re: [gmx-users] gromacs parallel doesn't work

maybe you should type: "grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o ResMD1 -np 4" and so "mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g ResMD1 > & ResMD1.job &" Beniamino Arneh Babakhani ha scritto: grompp -f ResMD1.mdp -c ../Heating/After

Re: [gmx-users] B-factor calculations

Jon Ellis wrote: Hello users I am using B-factors to look at protein flexibility, using g_rmsf. I have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I did g_rmsf on the complex using the -oq option to obtain the bfac.pdb file, which gives me the B-factors averaged over the ent