I'm interested in conducting umbrella sampling between a ligand and the center of mass of a lipid. Initially, I chose the atom numbers for the ligand and all the atom numbers for the lipids. However, due to the large number of lipid atoms, I observed a significant decrease in efficiency, achieving only 4 ns per day. Are there alternative approaches to achieve the same outcome with the typical performance of Amber?
The restraint input like that
Harmonic restraints for LIG and LIPID &rst iresid=0, fxyz=1,1,1, outxyz=0, iat=-1,-1, r1=59,r2=79,r3=79,r4=99, rk2=0.5, rk3=0.5, !! All LIG atoms igr1=36385,36386,36387,36388,36389,36390,36391,36392,36393,36394,36395,36396,36397,36398,36399,36400,36401,36402,36403,36404,36405,36406,36407,36408,36409,36410,36411,36412,36413,36414,36415,36416,36417,36418,36419,36420,36421,36422,36423,36424,36425,36426,36427,36428,36429,36430,36431,36432,36433,36434,36435,36436,36437,36438,36439,36440,36441,36442,36443,36444,36445,36446,36447,36448,36449,36450,36451,36452,36453,36454,36455,36456,36457,36458,36459,36460,36461,36462,36463,36464,36465,36466,36467,36468,36469,36470,36471,36472,36473,36474,36475,36476,36477,36478,36479,36480,36481,36482,36483, !! Some of the atom number of lipids igr2=4626,4627,4628,4629,4630,4631,4632,4633,4634,4635,4636,4637,4638,4639,4640,4641,4642,4643,4644,4645,4646,4647,4648,4649,4650,4651,4652,4653,4654,4655,4656,4657,4658,4659,4660,4661,4662,4663,4664,4665,4666,4667,4668,4669,4670,4671,4672,4673,4674,4675,4676,4677,4678,4679,4680,4681,4682,4683,4684,4685,4686,4687,4688,4689,4690,4691,4692,4693,4694,4695,4696,4697,4698,4699,4700,4701,4702,4703,4704,4705,4706,4707,4708,4709,4710,4711,4712,4713,4714,4715,4716,4717,4718,4719,4720,4721,4722,4723,4724,4725,4726,4727,4728,4729,4730,4731,4732,4733,4734,4735,4736,4737,4738,4739,4740,4741,4742,4743,4744,4745,4746,4747,4748,4749,4750,......,51183, /