Re: [gmx-users] Need Help on Simulated annealing (Implicit Solvation)

On 1/24/13 10:26 AM, Raghuvir R. S. Pissurlenkar wrote: Hi I have tried to write a grompp.mdp file for simulated annealing of a peptide (~30 aa) in implicit solvent. Please someone could tell me if the parameters set are fine for the same.

Re: [gmx-users] Need help with tabulated non-bonding potential tablep file

On 4/23/12 8:54 AM, Marcelo Lopez wrote: I get no answer so I insist... ¿Do my questions gets in to the email list? Your messages are arriving on the list. The documentation for tablep.xvg contents is certainly lacking, and unfortunately so too are the threads in the archive on the same t

Re: [gmx-users] need help with topology file

jampani srinivas wrote: Hi, I am trying to use two types of force fields for my system which has protein and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i don't have opls readily available for this). When i use two itp files in #include section grompp does not all

Re: [gmx-users] need help

On 23/05/2011 6:57 PM, rashi parihar wrote: Hi all I have an ligand having NI atom(Nickel) .Now problem is this when I am running PRODRG server ,ligand topology can not be created and error is coming *unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how to overcome this proble

Re: [gmx-users] Need help troubleshooting an mdrun-gpu error message!

Hi, There are two things you should test: a) Does your NVIDIA driver + CUDA setup work? Try to run a different CUDA-based program, e.g. you can get the CUDA SDK and compile one of the simple programs like deviceQuery or bandwidthTest. b) If the above works, try to compile OpenMM from source with

Re: [gmx-users] Need help!!!

users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 02, 2010 9:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Need help!!! #ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tuto

RE: [gmx-users] Need help!!!

your website also. ^_^ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 02, 2010 9:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Need

Re: [gmx-users] Need help!!!

#ZHAO LINA# wrote: Make sure your gromacs is the latest version. If not, update and try again. The tutorial is specifically written for version 4.0.5, but will be compatible with any version <4.5. Since the re-organization of the force field directories, the information provided in the tu

Re: [gmx-users] Need help!!!

praba vathy wrote: Hi, I am using simulation for a membrane protein. So i have downloaded the dppc.pdb along with it's topology files. I have used the following steps for the simulation (Based on the link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/

RE: [gmx-users] Need help!!!

Make sure your gromacs is the latest version. If not, update and try again. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] Sent: Thursday, September 02, 2010 9:06 PM To: gmx-users@gromacs.org

Re: [gmx-users] need help

- Original Message - From: Anamika Awasthi Date: Thursday, August 12, 2010 16:41 Subject: [gmx-users] need help To: gmx-users@gromacs.org > Dear gromacs user, > > I want to install gromacs new version on my linux system. can u all please > guide me, The GROMACS installation guide c

Re: [gmx-users] Need help with installation on Itanium2

Yep, my mistake, I built the serial version using gcc previously, so the problem really _is_ in Intel's compiler. I've finally figured out how to make mpicc use gcc instead of Intel, so now I have a working MPI version of GROMACS. Thank you again, Vasilii 2008/4/28 Mark Abraham <[EMAIL PROTECTED]

Re: [gmx-users] Need help with installation on Itanium2

Vasilii Artyukhov wrote: Thanks for quick reply, 2008/4/28 Mark Abraham <[EMAIL PROTECTED] >: Vasilii Artyukhov wrote: Dear everyone, I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a certain point, the compilation

Re: [gmx-users] Need help with installation on Itanium2

Thanks for quick reply, 2008/4/28 Mark Abraham <[EMAIL PROTECTED]>: > Vasilii Artyukhov wrote: > > > Dear everyone, > > > > I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a > > certain point, the compilation crashes with > > > > What hardware, compilers, GROMACS version an

Re: [gmx-users] Need help with installation on Itanium2

Vasilii Artyukhov wrote: Dear everyone, I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a certain point, the compilation crashes with What hardware, compilers, GROMACS version and configure command line were you using? Mark ___

Re: [gmx-users] Need help: error during installation

shyamala iyer wrote: Hi, I am new to GROMACS and I am having some trouble installing GROMACS in my home directory. The machine I am currently working on has fftw, gcc and binutils already installed fftw package installed: fftw3-3.0.1-4 gcc: gcc-c++-3.4.6-3.1 libgcc-3.4.6-3.1 compat-libgcc-2