[gmx-users] umbrella sampling tutorial
Ming Tang
m21.tang at qut.edu.au
Wed Mar 18 02:21:47 CET 2015
Hi Justin,
Thanks a lot. I can move forward now.
Recently, I am trying to pull a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large spring constant in Gromos96 53 a6. But I still don't know how to do this. Can you give me some advice?
Regards,
Ming
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, 18 March 2015 10:34 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
On 3/17/15 8:08 PM, Ming Tang wrote:
> Hi Justin,
>
> Here is the error message.
> tm at tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl Bareword found
> where operator expected at distances.pl line 8, near ""gmx distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group "Chain_A"
> (Missing operator before Chain_A?)
> String found where operator expected at distances.pl line 8, near "Chain_A" plus com of group ""
> Bareword found where operator expected at distances.pl line 8, near "" plus com of group "Chain_B"
> (Missing operator before Chain_B?)
> String found where operator expected at distances.pl line 8, near "Chain_B"' -oav dist${i}.xvg""
> syntax error at distances.pl line 8, near ""gmx distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group "Chain_A"
> Execution of distances.pl aborted due to compilation errors.
>
You can't nest " in a Perl script without using escape characters.
system("gmx distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group \"Chain_A\" plus com of group \"Chain_B\"' -oav dist${i}.xvg")
Otherwise, just run gmx distance on the trajectory. Using the conf*.gro files is sort of a roundabout way to do this, but since you'll (in theory) need them later, it's semi-convenient to generate the output this way.
-Justin
> Thanks,
> Ming
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
> Of Ming Tang
> Sent: Wednesday, 18 March 2015 8:14 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] umbrella sampling tutorial
>
> Yes, it can not run. But I can extract the COM of different conf.groone by one manually. Due to the time difference, I will update the error message when I get to the office.
> Thanks.
>
> Sent from my Huawei Mobile
>
> Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 3/17/15 6:48 AM, Ming Tang wrote:
>> Moring Justin,
>>
>> Many thanks to you.
>> Sorry for the confused expression and the late reply. Today, I run the simulation step by step following the tutorial again. It turned out that the code you gave me recovers the behavior of the SMD portion of the tutorial, and the problem is the distances.pl script. As the g_dist command has been changed to gmx distance and gmx select, I got the result that the COM between Chain_A and Chain_B was constant over time using the old version script.
>> Then, I tried to modify the script like this:
>> Change
>> system("gmx distance -s pull.tpr -f conf${i}.gro -n index.ndx -oav
>> dist${i}.xvg < groups.txt &>/dev/null"); to system("gmx distance -n
>> index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group "Chain_A"
>> plus com of group "Chain_B"' -oav dist${i}.xvg");} Unfortunately, the modified script can run.
>
> I don't know what this means. You mean it can't run? Produces an error?
> Please be specific. I can't help you if I don't know what the problem is.
>
> -Justin
>
>> Could you help to figure out this problem?
>> Regards,
>> Ming
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
>> Of Justin Lemkul
>> Sent: Monday, 16 March 2015 9:27 PM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] umbrella sampling tutorial
>>
>>
>>
>> On 3/15/15 9:57 PM, Ming Tang wrote:
>>> Dear Justin,
>>>
>>> I have tried many cases, and only your code runs smoothly. If I set pull-ngroups = 1, it will warn that pull-group2-name= Chain_A has not been defined.
>>> The code you gave me last time runs well. Though the COM between Chain_A and Chain_B remains the same over time, I found that Chain_A does dissociate from the structure and some particles fly away.
>>
>> It's the same, but things move apart? Sorry, this doesn't make sense to me. Do the .mdp settings I provided before recover the behavior of the SMD portion of the tutorial or not?
>>
>>> I am trying from the beginning once again and hope to find the reason. Besides, I got another problem. I want to probe the mechanical properties of a triple helix.
>>> I tried to fix one side (End) and pull the other side using the umbrella method:
>>>
>>> ; freeze groups
>>> freezegrps = End
>>> freezedim = Y Y Y
>>>
>>> ; COM pulling
>>> pull = umbrella
>>> pull-geometry = distance
>>> pull-dim = Y N N
>>> pull-start = yes
>>> pull-ngroups = 2
>>> pull-ncoords = 1
>>> pull-coord1-groups = 1 2
>>> pull-group1-name = End
>>> pull-group2-name = pull
>>> pull-coord1-rate = 0.005
>>> pull-coord1-k = 1000
>>>
>>> WARNING: Listed nonbonded interaction between particles 179 and 190 at distance inf which is larger than the table limit 2.437 nm.
>>>
>>> This is likely either a 1,4 interaction, or a listed interaction
>>> inside a smaller molecule you are decoupling during a free energy calculation.
>>> Since interactions at distances beyond the table cannot be computed,
>>> they are skipped until they are inside the table limit again. You
>>> will only see this message once, even if it occurs for several interactions.
>>>
>>> IMPORTANT: This should not happen in a stable simulation, so there
>>> is probably something wrong with your system. Only change the
>>> table-extension distance in the mdp file if you are really sure that is the reason.
>>>
>>
>> I'd venture a guess here that your system is probably blowing up because you're tugging on one molecule, which reaches a limit, distorts, and the simulation fails.
>>
>>> If I just fix one of the three dimensions, it can run around 100 steps. Then, I turned to use SMD method to pull the triple helix along x direction. I tried the following method to generate the box, but got a fatal error.
>>> editconf -f complex.gro -o newbox.gro -c -d 1 editconf -f
>>> complex.gro -o newbox.gro -center 5.63865 1.8837 1.9762 -box 20 3.8
>>> 4.0
>>>
>>> ; freeze groups
>>> freezegrps = End
>>> freezedim = Y Y Y
>>>
>>> ; COM pulling.
>>> pull = umbrella
>>> pull-geometry = direction-periodic
>>> pull-start = yes
>>> pull-ngroups = 2
>>> pull-ncoords = 1
>>> pull-coord1-groups = 1 2
>>> pull-group1-name = End
>>> pull-group2-name = pull
>>> pull-coord1-rate = 0.01
>>> pull-coord1-k = 1000
>>> pull-coord1-vec = 1 0 0
>>>
>>> Fatal error:
>>> Can not have dynamic box while using pull geometry
>>> 'direction-periodic' (dim x)
>>>
>>> Could you teach me how can I build a fixed box? And is my SMD code right?
>>>
>>
>> This means you can't use pressure coupling in the direction along which you're pulling. Use NVT or align the system such that you are pulling along z, in conjunction with semiisotropic coupling and zero compressibility along z.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences School of Pharmacy Health
>> Sciences Facility II, Room 629 University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list