From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Sep 01 2016 - 09:44:22 CDT
What are the values in the colvar file? Steadily increasing is fine if
they are going towards the target.
-Josh
On 09/01/2016 08:06 AM, Olya Kravchenko wrote:
> Hi Amy,
>
> thank you very much for your comments. I believe that atom numbers are
> correct. The values in the colvar file indeed look strange, they are
> steadily increasing (I'd expect them to oscillate around certain
> value?). I will try to implement forceNoPBC.
>
> Olga
>
>
> On Wed, Aug 31, 2016 at 11:40 AM, Amy Rice <arice3_at_hawk.iit.edu> wrote:
>> Hi Olga,
>> A few things I would look at:
>> 1) This may be obvious, but have you verified that the atom numbers
>> (especially for the ion) are correct? I had an issue in the past where the
>> atom numbers of the original pdb I used to set up the system differed from
>> the numbering in the NAMD files which caused me to pull on the wrong atom.
>> Another possible point of confusion is that VMD uses 0 indexing for atoms
>> whereas NAMD starts the count at 1. Just a few simple things to check, as
>> they have caused me some confusion in the past with umbrella sampling!
>> 2) The next thing I would check is that the distanceZ colvar values match up
>> with what you think they should be. Take a few steps in the trajectory and
>> verify that the colvar value printed in the colvar.traj file seem reasonable
>> based on visualizing the trajectory. This could hint if you perhaps have the
>> center or groups specified incorrectly.
>> 3) Finally, you can try turning "forceNoPBC" on. I believe if you don't
>> specify this, distances are calculated according to the minimum image
>> distance, rather than the proper distance in the unit cell. I believe this
>> is probably the issue you are having, since you note that the ion is being
>> pulled across the periodic boundary, and faster when the force constant is
>> higher. Again, see point 2 because if this is the case, the values in the
>> colvar.traj file will probably not match with your expectation based on
>> visualizing the trajectory.
>>
>> Hope this helps,
>> - Amy
>>
>> On Tue, Aug 30, 2016 at 4:17 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>> Hi all,
>>>
>>> I try to run Umbrella Sampling with harmonic restraints on a ion
>>> permeation through the pore in a spherical protein. What I see is that
>>> ion is escaping through the entrance (while it supposed to either
>>> oscillate around the same spot or proceed towards the next binding
>>> site; this happened for the first three windows).
>>>
>>> I assumed that my force constant is not high enough to hold the ion
>>> near the desired position, so I experimented with the force constant
>>> and increased it up to 10 times, but what I see is an even faster
>>> escape. The ion moves so fast that it leaves the simulation cell and
>>> enters from the other side of the simulation cell and tries to
>>> approach the channel at the exit. The higher the force constant the
>>> faster it moves.
>>>
>>> I've added upperboundary and lowerboundary to no avail.
>>>
>>> Here is my current colvar input file. Am I making a mistake somewhere?
>>> Is there a way to keep the ion within desired range?
>>>
>>>
>>> colvarsTrajFrequency 100
>>> colvarsRestartFrequency 100
>>>
>>>
>>> colvar {
>>>
>>> width 1.0
>>> lowerboundary 108.0
>>> upperboundary 136.0
>>> outputSystemForce yes
>>> outputAppliedForce yes
>>> name ferritin
>>> distanceZ {
>>> main {
>>> atomnumbers { 291491 }
>>> }
>>> ref {
>>> atomnumbers {
>>> 5 19 30 47 63 87 104 118 139 156 173 185 196 211 221 231 250 264 288
>>> 305 324 338 357 372 391 412 422 433 454 470 491 510 521 538 549 570
>>> 591 611 623 647 659 671 687 697 716 738 752 772 782 804 825 845 864
>>> 881 898 909 926 941 956 980 995 1012 1022 1037 1059 1078 1095 1117
>>> 1136 1153 1167 1184 1208 1215 1222 1246 1265 1285 1304 1321 1333 1352
>>> 1369 1393 1405 1417 1428 1440 1452 1476 1491 1502 1509 1528 1542 1552
>>> 1569 1584 1595 1605 1624 1641 1660 1675 1697 1711 1727 1741 1758 1769
>>> 1788 1807 1822 1841 1858 1880 1899 1909 1923 1935 1957 1971 1985 1997
>>> 2014 2033 2044 2056 2076 2095 2110 2124 2141 2162 2181 2195 2210 2227
>>> 2243 2265 2275 2294 2316 2331 2350 2357 2369 2386 2402 2416 2430 2449
>>> 2473 2495 2512 2519 2531 2543 2558 2569 2576 2595 2605 2620 2641 2660
>>> 2680 2692 2714 2731 2745 2764 2774 2788 2799 2816 2832 2856 2873 2887
>>> 2908 2925 2942 2954 2965 2980 2990 3000 3019 3033 3057 3074 3093 3107
>>> 3126 3141 3160 3181 3191 3202 3223 3239 3260 3279 3290 3307 3318 3339
>>> 3360 3380 3392 3416 3428 3440 3456 3466 3485 3507 3521 3541 3551 3573
>>> 3594 3614 3633 3650 3667 3678 3695 3710 3725 3749 3764 3781 3791 3806
>>> 3828 3847 3864 3886 3905 3922 3936 3953 3977 3984 3991 4015 4034 4054
>>> 4073 4090 4102 4121 4138 4162 4174 4186 4197 4209 4221 4245 4260 4271
>>> 4278 4297 4311 4321 4338 4353 4364 4374 4393 4410 4429 4444 4466 4480
>>> 4496 4510 4527 4538 4557 4576 4591 4610 4627 4649 4668 4678 4692 4704
>>> 4726 4740 4754 4766 4783 4802 4813 4825 4845 4864 4879 4893 4910 4931
>>> 4950 4964 4979 4996 5012 5034 5044 5063 5085 5100 5119 5126 5138 5155
>>> 5171 5185 5199 5218 5242 5264 5281 5288 5300 5312 5327 5338 5345 5364
>>> 5374 5389 5410 5429 5449 5461 5483 5500 5514 5533 5543 5557 5568 5585
>>> 5601 5625 5642 5656 5677 5694 5711 5723 5734 5749 5759 5769 5788 5802
>>> 5826 5843 5862 5876 5895 5910 5929 5950 5960 5971 5992 6008 6029 6048
>>> 6059 6076 6087 6108 6129 6149 6161 6185 6197 6209 6225 6235 6254 6276
>>> 6290 6310 6320 6342 6363 6383 6402 6419 6436 6447 6464 6479 6494 6518
>>> 6533 6550 6560 6575 6597 6616 6633 6655 6674 6691 6705 6722 6746 6753
>>> 6760 6784 6803 6823 6842 6859 6871 6890 6907 6931 6943 6955 6966 6978
>>> 6990 7014 7029 7040 7047 7066 7080 7090 7107 7122 7133 7143 7162 7179
>>> 7198 7213 7235 7249 7265 7279 7296 7307 7326 7345 7360 7379 7396 7418
>>> 7437 7447 7461 7473 7495 7509 7523 7535 7552 7571 7582 7594 7614 7633
>>> 7648 7662 7679 7700 7719 7733 7748 7765 7781 7803 7813 7832 7854 7869
>>> 7888 7895 7907 7924 7940 7954 7968 7987 8011 8033 8050 8057 8069 8081
>>> 8096 8107 8114 8133 8143 8158 8179 8198 8218 8230 8252 8269 8283 8302
>>> }
>>> }
>>> axis ( 0.0, 0.0, 1.0 )
>>> }
>>> }
>>>
>>> harmonic {
>>> colvars ferritin
>>> centers 130.0
>>> forceConstant 0.2
>>> # targetCenters 134.0
>>> # targetNumSteps 1
>>> }
>>>
>>>
>>> Olga
>>>
>>
>>
>> --
>> Amy Rice
>> Ph.D. Student
>> Physics Department
>> Illinois Institute of Technology
>
>
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