[gmx-users] g_sasa

Hey everyone... I need help I would like to know how to calculate the sasa (solvent accesible surface area). What quantum or statiscal method to calculate done that? Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX

[gmx-users] Fatal Error - RMSD Calculation

Hi everyone, I want to calculate the RMSD, and a few minutes to start the calculation, appears that Fatal Error: calloc for bond_mat[i] (nelem=50001, elsize=4, file gmx_rms.c, line 650) I don't have any idea what is the problem. Thanks in advance!!!... Deisy Y. Rodriguez S. Practicante de Comp

[gmx-users] XTC Error!!!

Hi Everyone!!! As you begin to operate the mdrun, appear time after Fatal Error: XTC Error To this happen? As can be fixed? Thanks in advance Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Tel. 6344000  ext. 2792 Uni

Re: [gmx-users] ffamber94 with gromacs 4.0.3

Yes, the force field Amber94 is compatible with Gromacs 4.0, i use that combination...you should are very careful whit the instalation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

[gmx-users] Help with Segmentation fault!!!

Hi everyone, I need help because when i run in gromacs, in a few seconds, appears "segmentation fault" i think that posibly is die to .mdp file. So is  copied below. thanks in advance. title    = cpp  = /usr/bin/cpp include  = define   

[gmx-users] Bind Free energy

Hi everyone!!! How is calculated the Bind Free Energy in Gromacs? With the sub-program g_lie? Thanks for your help Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Tel. 6344000  ext. 2792 Universidad Industrial de Sant

[gmx-users] Implicit Solvent

Hi everyone!!! Can I use implicit solvent in a MD simulations on gromacs? How can I do it? Thanks for your help!!! Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Tel. 6344000  ext. 2792 Universidad Industrial de Sant

[gmx-users] How is calculated the bind free energy GROMACS???

Hi, I need to know how to calculated GROMACS, the bind free energy, words, equations used to calculated the bind free energy in the sub-program g_lie. Thank you Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Te