Re: [gmx-users] Help for running gromacs

I will download latest version of gromacs and start working with it.I will be back if any face any problem. Thanks to all On Mon, May 3, 2010 at 6:39 PM, Justin A. Lemkul wrote: > > What compilers did you use to install Gromacs? Often times hangs and other > memory errors are related to buggy c

Re: [gmx-users] Help for running gromacs

What compilers did you use to install Gromacs? Often times hangs and other memory errors are related to buggy compilers. -Justin priyanka panwar wrote: Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul > wrote:

Re: [gmx-users] Help for running gromacs

-np is not about number of processors in the case of genion. It's the number of positive ions to insert. shaya...@post.tau.ac.il skrev: Hi, No need to include "-np 4" at all. genion command does not take advantage of multiple processors (nor does it need to). Try rerunning the command withou

Re: [gmx-users] Help for running gromacs

Hi, I tried it that way also, but in that case it displays a message "No ions to add and no potential to generate" and it is also not generating ions.pdb file but it is creating genion.log file. On Mon, May 3, 2010 at 6:02 PM, wrote: > Hi, > No need to include "-np 4" at all. genion command does

Re: [gmx-users] Help for running gromacs

Hi, No need to include "-np 4" at all. genion command does not take advantage of multiple processors (nor does it need to). Try rerunning the command without -np 4. -Shay Quoting "priyanka panwar" : Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Jus

Re: [gmx-users] Help for running gromacs

Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul wrote: > > > priyanka panwar wrote: > >> Hi, >> Thanks for help. >> -Command line was: >> Number of (3-Atomic) solvent molecules:4256 >> Replacing solvent molecule 499 (atom 2784) with Na >> >

Re: [gmx-users] Help for running gromacs

priyanka panwar wrote: Hi, Thanks for help. -Command line was: Number of (3-Atomic) solvent molecules:4256 Replacing solvent molecule 499 (atom 2784) with Na That's not a command line. What command did you actually type (exactly) to run genion? -Group selected was: 12 (SOL) -Gromacs vers

Re: [gmx-users] Help for running gromacs

Hi, Thanks for help. -Command line was: Number of (3-Atomic) solvent molecules:4256 Replacing solvent molecule 499 (atom 2784) with Na -Group selected was: 12 (SOL) -Gromacs version I am using is 3.3.1 On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk wrote: > Please post more details includin

Re: [gmx-users] Help for running gromacs

Please post more details including the following: - What is the exact command line? - What group do you select as a "continuous solvent"? I know it might sound weird to ask this but what I learned while teaching students is that these questions really should be asked when there are pro

[gmx-users] Help for running gromacs

I am using Gromacs for Simulation of Insulin.I have generated most of the files but unable to generate the ions.pdb file.The system is becoming idle after the Selection command. A line on the command prompt appears as "replacing solvent molecule with Na" and remains as such for many hours. Is this