[gmx-users] how to solve the warning

t; I don't know how to solve the problem. Jinyao Wang wan...@ciac.jl.cn 　　2009-05-25 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] some puzzled about the dihedral paramaters

602402 10 4 3 51 180.04.602402 11 54 61 180.0 4.602402 12 6 511 180.0 4.602402 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-

[gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

GMXLIB path variable) How can I solve it? Thank you in advance Jinyao Wang Ph.D. Candidate State Key Laboratory of Electroanalytical Chemistry ChangChun Institute of Applied Chemistry (CIAC) Chinese Academy of Sciences (CAS) Address: 5625 Renmin Street, Changchun 130022, P.R. China Tel

[gmx-users] -bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash: No such file or directory

ve it. 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-06-22 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] the warning about the -rerun

rerun.edr -g rerun.log It gives warings: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. How can I deal with the warning? Jinyao

[gmx-users] Energy analysis by mdrun -rerun

356.059570 1999.000122 -5333.074707 2000.000122 -5425.871582 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-07-01 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] puzzled about hydration free energy of Toluene

luene should be in the simulated system. 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-09-01 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] the problem about the calculation free energy of the toluene in water

nergy = yes init_lambda = 0.88 sc-alpha= 1.51 sc-power= 2.0 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-09-15 ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system

e problem and I want to know whether this method is effective for calculating the interaction between solvent and solvent in pure solvent system. Any suggestion will be appreciated. Jinyao Wang wan...@ciac.jl.cn 　

[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

> >Jinyao Wang wrote: >> Hi gmx-users锛? >> >> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and >> solvent in pure solvent system. After the simulation of my pure solvent >> system, I calculated the interaction between solvent and

[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (XAvier Periole)

gt;of your system seems to be what you are looking for! Hello XAvier. Thank you for your reply. Because I don't know how to set the option "energygrps" in rerun.mdp file, Now I still have no ideal for how to calculate the intermolecular interaction energy in pure solvent sy

Re: Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

imulation system is pure benzaldehyde system. I set the option nrexcl = 3. So I think the LJ and Coulombic terms include intermolecular interaction energy and intremolecular interaction eneryg (e.g. between atom and atom) Jinyao Wang wan...@

[gmx-users] why are the values of the LJ interaction energy negative and the values of the Coulomb interaction energy positive between two group.

interaction is repulsive. Is it correct for my consideration of the interaction ? Jinyao Wang wan...@ciac.jl.cn 　　2009-10-21 ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound

2.0 compressibility = 4.6e-5 ref_p = 1.0 ; Generate velocites is on at 323.15 K. gen_vel = yes gen_temp= 298.15 gen_seed = 173529 　　　 　Jinyao Wang wan...@ciac.jl.cn 　　2009-

[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (Justin A. Lemkul)

Dear Justin, Thank you for your help. I indeed didn't use the option "-nmol 512". > > >Jinyao Wang wrote: >> Hi gmx-users, >> I want to calcualted the the vaporation enthalpy of benzaldehyde >> I think that the the vaporation enthalpy is th

[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (David van der Spoel)

; and Could you talk about the details? >> >> Jinyao Wang wrote: >>> Hi gmx-users, >>> I want to calcualted the the vaporation enthalpy of benzaldehyde I >>> think that the the vaporation enthalpy is the sum of non-bond >>> interacion among

[gmx-users] I am not able to write the cyclohexane topology files

Hi, I want to carry out cyclohexane simulation with OPLS-AA. However, I am not able to write the cyclohexane topology files. If someone could sent me a cyclohexane OPLS-AA topology I'd very much appreciate it. 　　　　Jinyao Wang [

[gmx-users] I want to write the acetaldehyde topology files

！ Jinyao Wang [EMAIL PROTECTED] 　　2008-10-23 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

[gmx-users] how to set up a rigid system

Dear GMX users, I am carrying out MD for a rigid system by Gromacs.But I couldnot know how to set up this rigid system. If you could give me some advice or some material, I will appreciate it. Jinyao Wang [EMAIL PROTECTED

[gmx-users] seek for forcefield parameters

forcefield parameters of the acetaldehyde or some suggestion for me. Jinyao Wang [EMAIL PROTECTED] 　　2008-11-02 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] how to compute the shear viscosity

. I will appreciate it if you could give me some advice. 　Jinyao Wang [EMAIL PROTECTED] 　　2008-11-04 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] how to carry out the NEMD with gromacs to compute the shear viscosity

about NEMD, I will appreciate it. Jinyao Wang [EMAIL PROTECTED] 　　2008-11-05 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] how to write .top file for a rigid molecule

ow to write the .top file for the rigid Benzaldehyde. If you could give me some suggest, It is appreciated. 　　　　Jinyao Wang [EMAIL PROTECTED] 　　2008-11-12 ___ gmx-users mailing listgmx-users@gromac

[gmx-users] how to compute the solvent density distribution around solute and visulize it

about how to get the figure in the link. it is appreciated if you could give me some suggestion Jinyao Wang [EMAIL PROTECTED] 　　2008-12-09 ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] solvent spatial distribution

if I want to get a 3D solvent spatial distribution plot within r<=0.43nm, I don't know how to do it. Any suggestion will be appreciated. Happy New Year for everone in advance. 　Jinyao Wang wan...@ciac.jl.cn 　　20

[gmx-users] how to get a solvent density map using volumeslice in VMD

anything is displayed. how can I get the solvent density map? If you have some experience,please give me some suggestion. Jinyao Wang wan...@ciac.jl.cn 　　2009-02-13 ___ gmx-users mailing listgmx

[gmx-users] Re: Chris

85_0.bmp >So I use g_spatial to calculate the spatial distribution function and >get a *.cube file. >I load the *.cube file into VMD and view it as an volumeslice but no >anything is displayed. >how can I get the solvent density map? If you have some >experience,please

[gmx-users] Re:Re: g_spatial and vmd volume slice

lvent density map like that in the link >http://p13.freep.cn/p.aspx?u=v20_p13_p_0902131629052385_0.bmp >So I use g_spatial to calculate the spatial distribution function and >get a *.cube file. >I load the *.cube file into VMD and view it as an volumeslice but no >anything is disp

[gmx-users] how to convert the *.cube file to a (x, y, z) format file

hi gmx-users, I have run g_spatial and got a *.cube output file. But I don't know how to convert the *.cube file to a (x,y,z) format file in order to load it into other plot software. Any suggetion is appreciated 　　　　Jinyao Wang wan...@ciac.jl.cn 　　2009-

[gmx-users] Re:Re: how to convert the *.cube file to a (x, y, z) format file

files. Jinyao Wang 　　　 wan...@ciac.jl.cn 　 　 2009-02-26 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Question about g_hbond output

5.5 1 0 2006 1 0 2006.5 1 0 2007 1 1 2007.5 2 0 2008 1 0 2008.5 1 0 　　　 　 Jinyao