<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:bookman old style,new york,times,serif;font-size:12pt;color:#000000;"><div>Dear all...<br><br>I want to get spatial distribution function for ionic liquid. So, I used g_sdf command as below<br><br>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<br><br>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... <br><br>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.<br><br>[ C04 ]<br>2201<br><br>[ C06 ]<br>2185<br> <br>[ C08 ]<br>2192<br><br>[ ANION ]<br>4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 <br>4418
4419 4420 4421 4422 4423 4671 4672 4673 4674 4675 4676 4677 <br>4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4823 <br>4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 <br>4837 4838 4839 4840 4841 5051 5052 5053 5054 5055 5056 5057 5058 <br>5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5203 5204 <br>5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 <br>5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 <br>5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 <br>5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 <br>5257 5258 5259 <br><br>My question is, <br>
1) which -mode that i should used to get the probability density anion around cation in g_sdf?<br>2) Could anybody tell me what is the different between -mode 1, -mode 2 and -mode 3 in g_sdf? <br>3) what -mode is suitable for my ionic liquid?<br><br>Thanks....<br><br>IMA<br><br><br></div>
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