[gmx-users] fw: hey

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[gmx-users] FW: No subject

http://www.satoriholistichealth.com/uws/wd.fto?ntw Wholly Peach 4/3/2013 2:39:18 PM rl 4/3/2013 2:39:18 PM Wholly Peach -- gmx

[gmx-users] newest version of gromacs under cygwin

you on it.   Cheers,   Wholly From: Tsjerk Wassenaar To: Wholly Peach ; Discussion list for GROMACS users Sent: Saturday, 17 March 2012 6:06 PM Subject: Re: [gmx-users] Equilibriation nvt.mdp error Hi Wholly, It would be better to install a more recent

[gmx-users] Equilibriation nvt.mdp error

Dear All,   I am running the on-line tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html.   By "grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr", with the nvt.mdp downloaded as attached following, I got the following error message:   "creatin

Re: [gmx-users] genion -pname no NA molecule (sodium) type

molecule (sodium) type On 17/03/2012 4:48 PM, Wholly Peach wrote: >Dear All, >I use the following to neutralize the charge >"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn >8", >Then I do the following "grompp -f minim.mdp -c 1AK

[gmx-users] genion -pname no NA molecule (sodium) type

 Dear All, I use the following to neutralize the charge "genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8", Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"". However the feedback says there is no Na (sodium) moleculetype. I

[gmx-users] pdb2gmx error message

Dear All,   I meet the following error message for pdb2gmx. Please let me know how to solve this problem.   Cheers,   Wholly  Program pdb2gmx, VERSION 3.3.3 Source code file: futil.c, line: 542 Fatal error: Library file FF.dat not found in current dir nor in default directories. (You can set the d

[gmx-users] on the RAM capacity needed for GROMACS

Dear All, Suppose I need to install the GROMACS in my laptop. Will you please tell me the requirement on the capacity of RAM? Cheers, wholly-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] gromacs 3.3.3 and gromacs 4.5.5

Dear All, For the gromacs 3.3.3 and gromacs 4.5.5, for regular protein molecular dynamics simulation, will you please tell me the possible difference on their calculated results? Cheers, Fenghui-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] gromacs 4.5.5 cygwin installation error message

x/linux virtual machine with paravirt I/O? I'm not aware that anyone's compared them. Mark > > On 2012-03-12 11:21:26AM +1100, Mark Abraham wrote: >> On 12/03/2012 8:14 AM, Wholly Peach wrote: >>> Dear All, >>> For fftw, I use the following configure, >>

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

ject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message     On 12/03/2012 8:14 AM, Wholly Peach wrote: Dear All, >  >For fftw, I use the following configure, >  >./configure --enable-threads --enable-float --enable-sse >--prefix=/home/ABC/fftw If /home/ABC

[gmx-users] gromacs 4.5.5 cygwin installation error message

m: Mark Abraham To: Discussion list for GROMACS users Sent: Sunday, 11 March 2012 6:26 PM Subject: Re: Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message On 11/03/2012 7:03 PM, Wholly Peach wrote: Dear All, >  >Fot the fftw3, I use the following configuration, and make

Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message

cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1   - Forwarded Message - From: Peter C. Lai To: Wholly Peach ; Discussion list for GROMACS users Sent: Sunday, 11 March 2012 11:54 AM Subj

Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

installation error message On 11/03/2012 12:20 PM, Peter C. Lai wrote: > Is fftw3 properly installed in /usr/local/lib? And of the right precision, like reading the installation guides will warn you... Mark > > On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote: >>    Dea

[gmx-users] gromacs 4.5.5 cygwin installation error message

   Dear All,   For Gromacs installation, my configure command is:   ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly     . .libs/g