Re: [gmx-users] a strange behavior in editconf -rotate

Hi Dongsheng Zhang, Rotating the system with editconf does not change the box. It is likely that you rotated your molecule with respect to the box, such that you have caused severe overlaps. Glancing at your coordinates (notably z) and the box vectors supports this. Try creating a new box for the

[gmx-users] oplsaa and lincs error

Hi gmx users, I am trying to perform Free Energy calculations on a non-standard residue using oplsaa force field. Two problems arise: 1) When I try to minimize in vacuo, atoms split apart and molecule is destroyed. This is independent of the algorithm. I tried with and witohut constraints on the

Re: [gmx-users] Cannot compile Gromacs on Solaris

Now I use: export MPICC=/usr/local/lam/bin/mpicc export MPIF77=/usr/local/lam/bin/mpif77 export CC=/development/SUNWspro/bin/cc export F77=/development/SUNWspro/bin/f77 #export CC=/usr/local/gnu/gcc/3.2.3/bin/gcc #export F77=/usr/local/gnu/gcc/3.2.3/bin/g77 export LAMHOME=/usr/local/lam export CP

Re: [gmx-users] Cannot compile Gromacs on Solaris

Hi Mark, Did you do a make distclean and ./configure again? Sure. Now I try to compile with native Sun compilers. Maybe this is the problem. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] a strange behavior in editconf -rotate

Dear GMX users, I have generated a pdb file (test1.pdb) for a PPO chain. I can do energy minimization for this chain using oplsaa FF. However, if I rotate the chain by editconf -f test1.pdb -rotate 9 -9 0 -o test2.pdb then I can't do EM for test2.pdb. Could anyone tell me why the rotation of a

Re: [gmx-users] Cannot compile Gromacs on Solaris

MS wrote: Hi Mark, Some more meat: gcc 2.95 is pretty ancient... I'd suggest you get a real compiler and try again :-) Mark I change compiler to gcc 3.2.3. But: Some idea? Did you do a make distclean and ./configure again? Mark ___ gmx-users m

Re: [gmx-users] Cannot compile Gromacs on Solaris

Hi Mark, Some more meat: gcc 2.95 is pretty ancient... I'd suggest you get a real compiler and try again :-) Mark I change compiler to gcc 3.2.3. But: Some idea? Magda /usr/local/gnu/gcc/3.2.3/bin/gcc -DHAVE_CONFIG_H -I. -I. -I../../../src -I../../../include -DGMXLIBDIR=\"/home/magg/usr/gro

[gmx-users] Re: FEP softcore problematics

> Sorry about all of the confusion. Basically, the answer to this > depends on what exactly you're doing. (I should really write all of > this up in a tutorial soon). The way I think about it is that there > are two fundamental principles you need to keep in mind, and you can > do it any way you ca

[gmx-users] Problem simulating DNA

hi all i`m new to gromacs and am tyring to simulate a dna molecule. but i am facing following problem on running pdb2gmx A PORTION OF OUTPUT WARNING: atom H41 is missing in residue DCYT 47 in the pdb file You might need to add atom H41 to the hydrogen database of residue

Re: [gmx-users] how to add an element in Gromacs

Yongqiang Wang wrote: Dear guys, I am a new user of Gromacs. I am trying to do simulations of an organic molecular (say CH3CH2SH) absorption on the Gold Au111 surface. There is no data about gold information so I must add atomtype Au and add some relative force fields ( Au-Au, Au-S, Au

Re: [gmx-users] Cannot compile Gromacs on Solaris

MS wrote: Hi, I have a problem: After: gromacs-3.3.1$ ./configure --enable-shared --disable-float --prefix=/home/magg/usr/gromacs gcc 2.95 is pretty ancient... I'd suggest you get a real compiler and try again :-) Mark ___ gmx-users mailing list

[gmx-users] how to add an element in Gromacs

Dear guys,   I am a new user of Gromacs. I am trying to do simulations of an organic molecular (say CH3CH2SH) absorption on the Gold Au111 surface.   There is no data about gold information so I must add atomtype Au and add some relative force fields ( Au-Au, Au-S, Au-S-C, Au-S-C-C). Ho

[gmx-users] Cannot compile Gromacs on Solaris

Hi, I have a problem: After: gromacs-3.3.1$ ./configure --enable-shared --disable-float --prefix=/home/magg/usr/gromacs - and then make I got the following error: My LD_LIBRARY_PATH is gromacs-3.3.1$ echo $LD_LIBRARY_PATH /home/magg/usr/fftw/lib/: Do you have any idea what is g

Re: [gmx-users] Re: FEP softcore problematics

Sorry about all of the confusion. Basically, the answer to this depends on what exactly you're doing. (I should really write all of this up in a tutorial soon). The way I think about it is that there are two fundamental principles you need to keep in mind, and you can do it any way you can cook

Re: [gmx-users] grompp error

Hi, Mahnam Your top file could be wrong. Would you please paste here? Yang Ye Mahnam wrote: In God We Trust Hello Dear proof David van der Spoel I want to do energy minimization on bilirubin in HSA with OPLS force feid .Unfortunately x2top command doesn't work and I made topology file of