From: Liqun Zhang (lxz79_at_case.edu)
Date: Thu Dec 31 2020 - 15:55:27 CST
Thanks a lot! After switching to namd2.13b2 edition, it worked!
Lqz
On Thu, Dec 31, 2020 at 1:09 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> I agree with Josh, best to upgrade to the next stable version if
> possible. If you are using a supercomputer and relying
> on others to build codes, they may not have gotten around to installing
> 2.14 yet. If that is the case, 2.13 (released in Fall 2018) has the
> harmonicWalls features as well:
>
> https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_config_changes__;Iw!!DZ3fjg!pZtHkFg1VkM-ur7H7WCjkaOq03UhqhQwTmb2tBCUCzbqxTxBKWxLkQObpIu1hzihUw$
>
> Giacomo
>
> On Thu, Dec 31, 2020 at 1:09 PM vermaasj <vermaasj_at_msu.edu> wrote:
>
>> That is certainly a pertinent bit of info. I’d highly advise upgrading to
>> 2.14. In 2.12, the lowerWall, upperWall, and force constant arguments were
>> defined within the colvar itself.
>> https://www.ks.uiuc.edu/Research/namd/2.12/ug/node55.html#SECTION000132200000000000000
>>
>>
>>
>> -Josh
>>
>>
>>
>> *From: *Liqun Zhang <lxz79_at_case.edu>
>> *Date: *Thursday, December 31, 2020 at 1:05 PM
>> *To: *vermaasj <vermaasj_at_msu.edu>
>> *Cc: *namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
>> *Subject: *Re: namd-l: about geometrical restrain protein on membrane
>>
>> Hi,
>>
>> I did the test, but got the error message that
>>
>> harmonicWalls was not supported.
>>
>>
>>
>> I used namd 2.12. Thank you!
>>
>>
>>
>> Lqz
>>
>>
>>
>>
>>
>> On Thu, Dec 31, 2020 at 9:06 AM vermaasj <vermaasj_at_msu.edu> wrote:
>>
>> To my eyes, your setup looks overly complicated. This would be the colvar
>> I would write to try and keep the protein within 10 Angstroms of a membrane
>> plane:
>>
>>
>>
>> colvar {
>>
>> name prot_membrane_distance
>>
>> distanceZ {
>>
>> main {
>>
>> atomnumbers {17725 17852 18354 18857 18984 19111 19365 19492 19619
>> 19746 19873 20000 20375 20629 20754 20879 21133 21260 21387 21514 21641
>> 21768 21893 22020}
>>
>> }
>>
>> ref {
>>
>> atomNumbers { 5 743 1481 2219 2957 3695 4433 5171 5909 6647 7385 8123
>> 8861 9599 10337 11075 11813 12551 13289 14027 14765 15503 16241 16979 }
>>
>> }
>>
>> }
>>
>> }
>>
>>
>>
>> harmonicWalls {
>>
>> name tenangstromwalls
>>
>> colvars prot_membrane_distance
>>
>> lowerWalls -10
>>
>> upperWalls 10
>>
>> forceConstant 5
>>
>> }
>>
>>
>>
>> The key here is to use the “main” and “ref” selections so that you are
>> measuring the relative distance between the two groups, rather than using
>> dummy atoms and an arbitrary reference frame. Just remember to turn
>> wrapping off in NAMD, or the values calculated may not always be what you
>> expect. The harmonic walls constraint defines a flat-bottomed potential
>> that kicks in when you are more than 10 Angstroms away.
>>
>>
>>
>> -Josh
>>
>>
>>
>>
>>
>> *From: *owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu>
>> *Date: *Wednesday, December 30, 2020 at 10:40 PM
>> *To: *Namd Mailing List <namd-l_at_ks.uiuc.edu>
>> *Subject: *namd-l: about geometrical restrain protein on membrane
>>
>> Dear all:
>>
>>
>>
>> I want to restrain the protein center of mass distance from the membrane
>> surface to be no more than 10 A. I know in CHARMM we can set up a
>> geometrical plane to do that. I am wondering how to do that in namd? I set
>> up the colvar files as below, and I am wondering if it can work:
>>
>>
>>
>> colvar {
>>
>> name memb_plane
>>
>> distanceZ {
>>
>> axis (0.0, 0.0, 1.0)
>>
>> main {
>>
>> atomnumbers {17725 17852 18354 18857 18984 19111 19365 19492 19619
>> 19746 19873 20000 20375 20629 20754 20879 21133 21260 21387 21514 21641
>> 21768 21893 22020}
>>
>> }
>>
>> ref { dummyAtom ( 0.0, 0.0, 0.0 ) }
>>
>> }
>>
>> }
>>
>>
>>
>> colvar {
>>
>> name prot_cyl
>>
>> distanceZ {
>>
>> axis (0.0, 0.0, 1.0)
>>
>> main { atomNumbers { 5 743 1481 2219 2957 3695 4433 5171 5909 6647
>> 7385 8123 8861 9599 10337 11075 11813 12551 13289 14027 14765 15503 16241
>> 16979 }
>>
>> }
>>
>> ref { dummyAtom ( 0.0, 0.0, 10.0 ) }
>>
>> }
>>
>> }
>>
>>
>>
>> harmonic {
>>
>> colvars memb_plane prot_cyl
>>
>> centers 0.0 0.0
>>
>> forceConstant 5.0
>>
>> }
>>
>>
>>
>> I am wondering if above can work. Thank you for your time!
>>
>>
>>
>> Lqz
>>
>>
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