[gmx-users] spatial distribution function for ionic liquid

[naimah haron naimah]

Dear all...

I want to get spatial distribution function for ionic liquid. So, I used g_sdf command as below

g_sdf -f mixture_mdpr.trr -n index.ndx -s mixture_mdpr.tpr -o sdf_plt.dat -r sdf.gro -mode 1 -grid 3.8 3.8 3.8

I rename the output file from .dat file to .plt file and I used VMD to view the 3-D structure. The 3-D structure seems like not correct... 

The ionic liquid that I use is tetraethylammonium L-glutaminate.. I already create 4 group for index file. The first three groups comes from cation which is [C04], [C06] and [C08] and the last group, which is group 4 comes from anion.

[ C04 ]
2201

[ C06 ]
2185

[ C08 ]
2192

[ ANION ]
4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 
4418 4419 4420 4421 4422 4423 4671 4672 4673 4674 4675 4676 4677 
4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4823 
4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 
4837 4838 4839 4840 4841 5051 5052 5053 5054 5055 5056 5057 5058 
5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5203 5204 
5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 
5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 
5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 
5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 
5257 5258 5259 

My question is, 
1) which -mode that i should used to get the probability density anion around cation in g_sdf?
2) Could anybody tell me what is the different between -mode 1, -mode 2 and -mode 3 in g_sdf? 
3) what -mode is suitable for my ionic liquid?

Thanks....

IMA


      
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