gromacs遇到的问题
这是我的md.mdp文件的一部分。Tcoupl =berendsen
tau_t =0.1
0.1
tc_grps
=14Asol
ref_t =300300
annealing =single single
annealing_npoints =3 4
annealing_time = 051030 0 5 10 30
annealing_temp = 293 373 373 277 293 373 373 277
错误提示是：
Program grompp_mpi, VERSION 4.0.4
Source code file: readir.c, line: 1508
Fatal error:
Found 0 annealing-npoints values for 2 groups
首先要仔细阅读说明书：
Simulated annealing is controlled separately for each temperature group in GROMACS. The reference temperature is a piecewise linear function, but you can use an arbitrary number of points for each group, and choose either a single sequence or a periodic behaviour for each group. The actual annealing is performed by dynamically changing the reference temperature used in the thermostat algorithm selected, so remember that the system will usually not instantaneously reach the reference temperature!
annealing:
Type of annealing for each temperature group
no
No simulated annealing - just couple to reference temperature value.
single
A single sequence of annealing points. If your simulation is longer than the time of the last point, the temperature will be coupled to this constant value after the annealing sequence has reached the last time point.
periodic
The annealing will start over at the first reference point once the last reference time is reached. This is repeated until the simulation ends.
annealing-npoints:
A list with the number of annealing reference/control points used for each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.
annealing-time:
List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in annealing-npoints.
annealing-temp:
List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in annealing-npoints.
OK, let's use an example. Assume you have two temperature groups, set the group selections to annealing = single periodic, the number of points of each group to annealing-npoints = 3 4, the times to annealing-time = 0 3 6 0 2 4 6 and finally temperatures to annealing-temp = 298 280 270 298 320 320 298. The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by grompp if you are unsure!
你的这三项不对应，所以会导致问题。annealing_npoints =3 4
annealing_time = 051030 0 5 10 30
annealing_temp = 293 373 373 277 293 373 373 277
annealing_npoints =3 4 应改为annealing_npoints =4 4
4 4 要对应下面的 0 5 10 30 有四组，温度也有四组。
川大-灰太狼 发表于 2015-7-1 09:36
首先要仔细阅读说明书：
Simulated annealing is controlled separately for each temperature group in GR ...
你好，首先谢谢你的解释，不过我按照你的解释做了修改，可是结果还是一样的错误，不知道为何？？？你有什么好的建议嘛？谢谢 川大-灰太狼 发表于 2015-7-1 09:36
首先要仔细阅读说明书：
Simulated annealing is controlled separately for each temperature group in GR ...
按照你的解释同样会报错Found 0 annealing-npoints values for 2 groups
你有这方面的认识的朋友吗？可不可以帮我一下？问问是什么原因？ yuyang 发表于 2015-7-2 23:57
按照你的解释同样会报错Found 0 annealing-npoints values for 2 groups
你有这方面的认识的朋友吗？可 ...
你如何修改的呢？ 川大-灰太狼 发表于 2015-7-3 00:37
你如何修改的呢？
; Temperature coupling is on
tcoupl =Berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
annealing = single periodic
annealing‐npoints = 44
annealing‐time = 0 10 20 55 0 10 20 55
annealing‐temp = 300 313 323 293 300 313 323 293
Fatal error:
Found 0 annealing-npoints values for 2 groups
yuyang 发表于 2015-7-3 08:26
; Temperature coupling is on
tcoupl =Berendsen ; modified Berendsen thermostat
tc-grps = Prote ...
annealing = single periodic你不是改为了single single ，为啥有改为了 single periodic？
请仔细阅读下 single和periodic的区别。 川大-灰太狼 发表于 2015-7-3 10:14
annealing = single periodic你不是改为了single single ，为啥有改为了 single periodic？
请仔细 ...
即使是single single 错误还是一样的！！！不解啊！！！ 川大-灰太狼 发表于 2015-7-3 10:14
annealing = single periodic你不是改为了single single ，为啥有改为了 single periodic？
请仔细 ...
你有没有这方面mdp文件？有的话发我一份，邮箱为wyangdao@163.com
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