[gmx-users] Re: gmx-users Digest, Vol 92, Issue 66

On 13/12/2011 11:46, gmx-users-requ...@gromacs.org wrote: Message: 1 Date: Tue, 13 Dec 2011 17:10:01 +1100 From: Mark Abraham Subject: Re: [gmx-users] Force field for polymer molecule - tips To: Discussion list for GROMACS users Message-ID:<4ee6ec39.2090...@anu.edu.au> Content-Type: text/plain;

[gmx-users] mdrun stuck with PME on BlueGene/P

Dear all, I have compiled the gromacs 4.5.5 version on BlueGene/P both on the front end and bgp using the following script : with the front end as an example -- version=$1 PREFIX=/home/users/wur

[gmx-users] Gromacs 4.0.7 on Blue Gene/P

I also asked the administrator to install for me, the results were the same. Does anyone have similar experience? -- Yours Sincerely, Rongliang Wu Postdoc in K.U.Leuven -- Molecular and

[gmx-users] center of masses inappropriate

boundary. i wonder how to tackle this problem? Regards! Rongliang Wu wur...@iccas.ac.cn 　　2008-12-24 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] The g_sdf in gromacs 3.3.3

g_sdf program in gromacs3.3.3 seems problematic, and how shall i change the code? Regards! Rongliang Wu [EMAIL PROTECTED] 　　2008-07-30 ___ gmx-users mailing listgmx-users

[gmx-users] BHIS for HIS?

the binding of surfactants with the peptide. what are the difference? is there anywhere i can find the detailed description for these residues? Rongliang Wu [EMAIL PROTECTED] 　　2007-04-11

[gmx-users] slight mistake in data angdist.xvg file

hello, gmx-users i'd here report everyone that when calculating the R_B dihedral distribution using g_angle command, the resulting sum of the proportions listed in angdist.xvg has a value of 2, which should be 1 for a normalized distribution. 　　　　Rongliang Wu [

[gmx-users] RE RE:fugeQQ in buckingham

i have a polymer force field with the buckingham potential, and i still need a solvent(acetone and DMA) potenital with buckingham potential since Gromacs cannot use both buckingham and L-J for one system. i did not find such foce fields for acetone and DMA. and i have chosen to change the param

[gmx-users] simulations of crystal cell possible?

hello everyone, does anybody know how to simulate crystal cells in gromacs? since the cell size has to be no smaller than twice the cutoff. and if cutoff is too small, the program terminates because of the thus caused too high energy. my cell is very small about 0.7 nm. regards! Rongliang Wu

[gmx-users] the gmxdump reveals less parameters than i expect

! Rongliang Wu [EMAIL PROTECTED] 　　2006-09-13 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or se

[gmx-users] cross terms!!

or my system the same with those in literature. regards! thanks! 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-09-12 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

[gmx-users] changing the parameter numbers for torsion

hello,gmx-users i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? and where i should change the source code? regards! thanks! Rongliang Wu [EMAIL

[gmx-users] g_h2order still makes problem

mistakes from the index? my index file has only one group of the sequence OW HW1 HW2, the shell is not included. Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-05-24 ___ gmx-users mailing

[gmx-users] g_h2order problem

91357 waters in slice 98 91222 waters in slice 99 100 slices Back Off! I just backed up order.xvg to ./#order.xvg.6# gcq#215: "I've Got Two Turntables and a Microphone" (B. Hansen) 　　 Regards Thanks 　　　　　　　　Rongliang Wu [EMAIL PROTECTED] 　　

[gmx-users] simulation of long chains in vacuum

Rongliang Wu [EMAIL PROTECTED] 　　2006-05-10 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www inte

[gmx-users] umbrella search and ffscan, how?

? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-30 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

[gmx-users] after g_morph, how to calculate energies?

ypropelene(two chain unites), how can i get those conformations which might be beyond the ability of g_morph? Regards Thanks 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-04-30 ___ gmx-users mailing l

[gmx-users] conformation search

Hello, gmx-users， is it possible to do conformation searches using gromacs? and how? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-29 ___ gmx-users mailing listgmx-users

[gmx-users] pdb2gmx error

ere are no H2 atom in my file. why? my version is gromacs3.3 Regards Thanks 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-04-19 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/li

[gmx-users] position restraints

= -DPOSRES_B will restrian only A how to add both? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-14 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.or

Re: [gmx-users] grompp error

set the GMXLIB, it still doesnot work. and the md5sum was correct! i installed a send time and it didnot change Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-09 ___ gmx

[gmx-users] grompp error

le ""ao7.top"", line 13 --- it is clear that the program still cannot find the itp files in the top folder? why? is there anyother environmental variables that i didnot set ? Regards Thanks Ronglian

[gmx-users] still compilation problem

detected. Your build may be incomplete. and the gromacs thus installed has much problem! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-07 ___ gmx-users mailing listg

[gmx-users] grompp error

Name GROningen MAchine for Chemical Simulation [ molecules ] ; Compound#mols Protein 1 i also met with the same problem using gromacs-3.2 why? Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-07 _

[gmx-users] compile problem

Hello, gmx-users， i compiled a mpi gromacs-3.3 in a supercompuer and each make end with such warning: " make: warning: Clock skew detected. Your build may be incomplete." why ? and will it cause any futher problem? Regards Thanks 　　　　Ro

[gmx-users] 3.3mannual

Hello, david since you've changed the mannual then where can i get it? the website and the ftp has not been changed Regards Thanks 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-04-05 __

[gmx-users] problem caused by removed [ pairs ] in OPLS

l with or without [ pairs ] listed using OPLS, BUT the results didn't seem to have much difference! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-05 ___ gmx-users mailing listgmx-use

[gmx-users] lincs warning

system collapsed. i was using oplsaa force field and the [ pairs ] are removed as refered by the mannual i wonder where the problem might exists. any suggestion will be greatly appreciated! Regards Thanks Rongliang Wu [EMAIL PROTECTED] 　　2006-04-04

[gmx-users] chain construction

rom a small molecule? and which commands? Regards Thanks 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-03-28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] pdb2gmx problem

ds Thanks 　　　　Rongliang Wu [EMAIL PROTECTED] 　　2006-03-28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the lis

[gmx-users] grompp problem

-- Program grompp, VERSION 3.3 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated ------- -- Rongliang Wu 2006-03-21

[gmx-users] mpi problem

mpi is LAM -- Rongliang Wu 2006-03-20 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can&#x

[gmx-users] keep atoms planar

torsion. CA is any ring carbon (CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*) #define improper_Z_CA_X_Y 180.0 4.60240 2 are X Y Z designate any atom types? -- Rongliang Wu 2006-03-14 ___ gmx-users mailing list

[gmx-users] Rychaert-Belleman's dihedral

n the "fun 3" keep the stoms of the benzene within the plane? is it necessary to use Rychaert-Belleman's dihedral for the oplsaa force filed? Regards! -- Rongliang Wu 2006-03-14 ___ gmx-

[gmx-users] the manual

hello david, since the 3.3 version has changed much and been distributed for half a year, when will the mannual for 3.3 come out? -- Rongliang Wu 2006-03-02 ___ gmx-users mailing listgmx-users