[gmx-users] how to deduce charges for gromos forcefield?

Dear gmx-users, I want to develop an itp file for an organic molecule which has 87 atoms. I deduced the charge using the common Resp procedure with RED-III tool.However , I am not quite sure if the Resp charge or Esp charge can be used in Gromos forcefield, if not, how does Gromos forcefied dedu

[gmx-users] What is the relationship between simulation time

Thanks very much, what you have mentioned are situations which are temperature fixed. How about the molecular rearrangement when temperature is changed , for example, a lipidbilayer equilibrated at a temperature and then put it at another temperature? I know when I do this kind of simulations ,

[gmx-users] What is the relationship between simulation time and real time

Dear gmx-users, I have a basic question to propose: What is the relationship between simulation time and the actual time a real process occurs? Are they the same? Or do they have certain correlation in certain situation? Any suggestion will be appreciated, thanks in advance. _

[gmx-users] anisotropic pressure coupling for temperature annealing

Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there

[gmx-users] g_sas halted

Thanks for reply.I use Fedora Core 5 and gcc 4.1. Is that the problem? ___ 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! Pleas

[gmx-users] g_sas halted

Dear gmx-users.Today I want to use g_sas to analyse the DPPC surface area per lipid, however the program halted. My sytem consisted of lipid bilayer and water,and I used g_sas like this: g_sas -f run -s run Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Opening library f

[gmx-users] how to deal with large pressure fluctuation

Dear gmx-users: I made a lipid bilayer fully hydrated by water,without water in the lipid hydrophobic tails.Then I minimized the energy to Fmax=132.5,then I ran NVT md for 200ps.However when I wanted to run NPT simulation, the pressure fluctuation was as high as 1.33*10E+05,it crashed very easily

[gmx-users] energy minimization using double precision gromacs failed

Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of 32 lipids(16 up and 16 down) with two water layers(428 up and 428 down). my em.mdp is like this: title= cpp = /lib/cpp include = define = -DFLEXIBL

[gmx-users] a basic question

Mark,thanks very much. I will follow your suggestion and check wiki.gromacs.org.___ 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

[gmx-users] a basic question

hi,yang ye,I used the em.mdp you gave me before.It seemed like to have "none"there and worked well with other systems. Regards shanshan___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please sear

[gmx-users] a basic question

Hello everyone, I met with a probelm today.I want to simulate dppc lipid in water, however when I want to do energy minimization the grompp displayed "number of coordinates in the coordinate file (box.gro, 8253) does not match topology (topol.top, 0).I have checked the input file several times b

[gmx-users] a basic question

Hello everyone, I met with a problem today. I tried to simulate dppc lipid in water.However, when I want to minimize energy ,the grompp showed the error message like this: "number of coordinates in coordinate file (box.gro 8253 ) doesn't match topology ( topol.top , 0 ). I have used gromacs for