[gmx-users] help-Test set

Dear all, I installed gromacs-4.0.4, I followed the installation instruction. the installation seemed no problem at all. afterwards, I run test-set gmxtest-4.0.4 immediately. The results are All 16 simple tests PASSED FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check file

[gmx-users] Test-set

be. Thanks. Johnny Zhanglin Ni wrote: Dear all, I installed gromacs-4.0.4, I followed the installation instruction. the installation seemed no problem at all. afterwards, I run test-set gmxtest-4.0.4 immediately. The results are All 16 simple tests PASSED FAILED. Check files in field FAILED. C

[gmx-users] Test-set

.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Any clues from any of the other *.out files? -Justin Zhanglin Ni wrote: Thanks for your reply. I checked the checkpot.out file. It didnot show the any energy values but " comparing energy file reference_s.edr and ener.edr

[gmx-users] Test-set

MACS users Message-ID: <4a038ff5.3030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Zhanglin Ni wrote: The checkvir.out files looked like (I just show last few lines here): Pressure (bar) step 50: 46893.3, step 50:44603 Vir-XY step 5

[gmx-users] Test-set

080...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Zhanglin Ni wrote: The configurations are Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2 20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009 CPU1: Intel(R) Core(TM)2 Duo CPU

[gmx-users] Warning: Pressure scaling more than 1%.

Dear all, when I run position-restrained simulation (total 15000steps). when it reached 740 steps Step 741 Warning: Pressure scaling more than 1%. Step 742 Warning: Pressure scaling more than 1%. Step 743 Warning: Pressure scaling more than 1%. Step 744 Warning: Pressure scaling more than

[gmx-users] Coordinate covalent bond

Dear all, In pdb file. the metal ion form a coordinate covalent bond with SG of cystine. but seems pdb2gmx ignored CONNECT in pdb file. how to modify the .top or .itp to include the bond and parameterize the bond. I tried to find some tutorial for some special case like this. But I couldnot. C

[gmx-users] parameter for iron(HEME) and S-Cys

Dear all, The pdb2gmx can find the special bonds such as the coordinate covalent bond between CYS-S and Iron of HEME, but the library for example ffG53a6bon.itp doesnot contains the parameters for bond angle such as S-Fe-NR(heme), bond or dihedral torsional angles. Any suggestion to get the

[gmx-users] question about force field parameter

Dear all I am a little confused with some force field parameter library. for example #define gd_26 0.000 2.93 3 ; -CH2-S- 0.7 dihedral is supposed to be i j k l 4 atoms , why, for example, the case above has only 2 atoms. thanks Johnny

[gmx-users] Re: question about force field parameter

list for GROMACS users Message-ID: <4a18ec5b.6060...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Zhanglin Ni wrote: Dear all I am a little confused with some force field parameter library. for example Whether and how this makes sense depends on the context,

[gmx-users] force field parameter for ligands

Dear all, where do you usually get topolgy for small molecule ligand or do it manually? Dundee PRODRG Server seems to be capable of making .top for ffgmx only but not new ones like ffG53a6,etc. Thanks Johnny ___ gmx-users mailing listgmx-users@g