Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 7/6/18 10:42 AM, hosein geraili wrote:

Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash script to 
create the summary_distances.dat, but the problem is at first I would get the error 
"Unknown command-line option -o", then I used -oh instead of -o which worked, 
but the problem is the summary_distances.dat file is not correct, and it seems like:


-oh produces a histogram, not the distances themselves. Use -oall. I 
have fixed the script in the tutorial. Sorry for the typo.


-Justin


0 1 2 3 4 5 6 7 8 9 10 11 ...265 1000.000266 1000.000267 1000.000268 1000.000269 1000.000270 1000.000271 1000.000272 1000.000273 1000.000274 1000.000275 1000.000276 1000.000277 1000.000278 1000.000279 1000.000...10 tail -n 1 dist${i}.xvg | awk "{print 
$2}"11 tail -n 1 dist${i}.xvg | awk "{print $2}"12 tail -n 1 dist${i}.xvg | awk "{print $2}"13 tail -n 1 dist${i}.xvg | awk "{print $2}"14 tail -n 1 dist${i}.xvg | awk "{print $2}"15 tail -n 1 dist${i}.xvg | awk 
"{print $2}"16 tail -n 1 dist${i}.xvg | awk "{print $2}"17 tail -n 1 dist${i}.xvg | awk "{print $2}"18 tail -n 1 dist${i}.xvg | awk "{print $2}"19 tail -n 1 dist${i}.xvg | awk "{print $2}"20 tail -n 1 
dist${i}.xvg | awk "{print $2}"21 tail -n 1 dist${i}.xvg | awk "{print $2}"22 tail -n 1 dist${i}.xvg | awk "{print $2}"23 tail -n 1 dist${i}.xvg | awk "{print $2}"24 tail -n 1 dist${i}.xvg | awk "{print $2}"25 
tail -n 1 dist${i}.xvg | awk "{print $2}"26 tail -n 1 dist${i}.xvg | awk "{print $2}"27 tail -n 1 dist${i}.xvg | awk "{print $2}"...172 1000.000173 1000.000174 1000.000175 1000.000176 1000.000177 1000.000178 1000.000179 
1000.000180 1000.000181 1000.000182 1000.000183 1000.000184 1000.000185 1000.000...
What is the problem?Best


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==


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Re: [gmx-users] Umbrella sampling tutorial WHAM issue

[Justin Lemkul]

On 11/10/16 10:46 AM, Lindsay, Richard J. wrote:

Hi,

I am attempting to follow the gromacs umbrella sampling tutorial but have run 
into an issue at the data analysis step.

When I run the gmx wham command I get only one histogram, even though I 
collected 24 umbrella trajectories.



You're probably just plotting it wrong.  xmgrace -nxy histo.xvg, not xmgrace 
histo.xvg.


-Justin


Here is the command I am running:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

The *-files.dat files each contain a list of the 24 relevant files as such:

pullf-files.dat:

pullf-umbrella0.xvg
...
...
pullf-umbrella23.xvg


tpr-files.dat:
umbrella0.tpr
...
...
umbrella23.tpr


When I run the analysis on one .tpr/.xvg file at a time and run the analysis 24 
times I am able to combine the histograms produced to get the expected result: 
24 well-spaced histograms with reasonable overlap. However I would like to know 
why I am unable to get this result by running gmx wham once as in the tutorial. 
I am using gromacs 5.1.2.


Here is the log file from my original attempt at the wham analysis:

--

Note: Will use 32 OpenMP threads.

Found 24 tpr and 24 pull force files in tpr-files.dat and pullf-files.dat, 
respectively
Reading 12 tpr and pullf files
Automatic determination of boundaries...
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 
dimensions)
Pull group coordinates not expected in pullx files.
crd 0) k = 1000   position = 0.489812
Use option -v to see this output for all input tpr files

Reading pull force file with pull geometry distance and 1 pull dimensions
Expecting these columns in pull file:
0 reference columns for each individual pull coordinate
1 data columns for each pull coordinate
With 1 pull groups, expect 2 columns (including the time column)

Determined boundaries to 0.445155 and 5.253408

Wrote histo.xvg
Getting initial potential by integration.
Initialized rapid wham stuff (contrib tolerance 4.16667e-08)
Evaluating only 1013 of 4800 expressions.

   1) Maximum change 5.820592e-01
 100) Maximum change 6.205472e-03
 200) Maximum change 1.677333e-03
 300) Maximum change 1.011720e-03
 400) Maximum change 6.767362e-04
 500) Maximum change 5.057361e-04
 600) Maximum change 3.887035e-04
 700) Maximum change 3.053506e-04
 800) Maximum change 2.443217e-04
 900) Maximum change 1.986103e-04
1000) Maximum change 1.689707e-04
1100) Maximum change 1.467826e-04
1200) Maximum change 1.293663e-04
1300) Maximum change 1.141341e-04
1400) Maximum change 1.008461e-04
1500) Maximum change 8.925561e-05
1600) Maximum change 7.913347e-05
1700) Maximum change 7.036949e-05
1800) Maximum change 6.276724e-05
1900) Maximum change 5.603027e-05
2000) Maximum change 5.005392e-05
2100) Maximum change 4.474645e-05
2200) Maximum change 4.119858e-05
2300) Maximum change 3.794030e-05
2400) Maximum change 3.486749e-05
2500) Maximum change 3.199419e-05
2600) Maximum change 2.932535e-05
2700) Maximum change 2.685949e-05
2800) Maximum change 2.459074e-05
2900) Maximum change 2.251030e-05
3000) Maximum change 2.060762e-05
3100) Maximum change 1.887118e-05
3200) Maximum change 1.728904e-05
3300) Maximum change 1.584933e-05
3400) Maximum change 1.454045e-05
3500) Maximum change 1.335133e-05
3600) Maximum change 1.227147e-05
3700) Maximum change 1.129108e-05
3800) Maximum change 1.040106e-05
3900) Maximum change 9.593003e-06
4000) Maximum change 8.859203e-06
4100) Maximum change 8.192607e-06
4200) Maximum change 7.586786e-06
4300) Maximum change 7.035893e-06
4400) Maximum change 6.534625e-06
4500) Maximum change 6.078177e-06
4600) Maximum change 5.662203e-06
4700) Maximum change 5.282778e-06
4800) Maximum change 4.936358e-06
4900) Maximum change 4.619747e-06
5000) Maximum change 4.330065e-06
5100) Maximum change 4.064716e-06
5200) Maximum change 3.821363e-06
5300) Maximum change 3.597901e-06
5400) Maximum change 3.392435e-06
5500) Maximum change 3.203261e-06
5600) Maximum change 3.028843e-06
5700) Maximum change 2.867799e-06
5800) Maximum change 2.718886e-06
5900) Maximum change 2.580983e-06
6000) Maximum change 2.453083e-06
6100) Maximum change 2.334276e-06
6200) Maximum change 2.223746e-06
6300) Maximum change 2.120755e-06
6400) Maximum change 2.024637e-06
6500) Maximum change 1.934795e-06
6600) 

Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Any idea on this topic?

Thanks
> On 07 Oct 2016, at 14:13, gozde ergin  wrote:
> 
> Thanks Justin.
> I want infinite dilute bulk that’s why I do not want any surfactant molecule 
> inside the bulk.
> I may put a ‘’wall’’ just below the surface molecules in order to inhibit 
> their travel to bulk but I do not know how to remove this effect from PMF.
> 
> 
>> On 07 Oct 2016, at 13:40, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 10/7/16 4:41 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I would like to ask a question about Justin’s tutorial. By using the
>>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>>> effect of this restraint removed during the WHAM?
>>> 
>> 
>> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
>> the fact that there are only five peptides, when in reality, there are 
>> millions, so the effects of the forces are quite different in vitro/in vivo. 
>>  Restraining one peptide makes the remaining four peptides more stable, more 
>> realistic.  WHAM doesn't do anything to change this.
>> 
>>> I want to do a similar thing by applying restraint force on the organic
>>> molecule on the bulk water in order to inhibit their movement inside the
>>> bulk. Should I consider the removing of the restraint in PMF?
>>> 
>> 
>> In the case of freely diffusing molecules, I suspect such a restraint would 
>> have a much more profound impact.  Why do you want to do this?
>> 
>> -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
>> 
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
>> -- 
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Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Thanks Justin.
I want infinite dilute bulk that’s why I do not want any surfactant molecule 
inside the bulk.
I may put a ‘’wall’’ just below the surface molecules in order to inhibit their 
travel to bulk but I do not know how to remove this effect from PMF.


> On 07 Oct 2016, at 13:40, Justin Lemkul  wrote:
> 
> 
> 
> On 10/7/16 4:41 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I would like to ask a question about Justin’s tutorial. By using the
>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>> effect of this restraint removed during the WHAM?
>> 
> 
> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
> the fact that there are only five peptides, when in reality, there are 
> millions, so the effects of the forces are quite different in vitro/in vivo.  
> Restraining one peptide makes the remaining four peptides more stable, more 
> realistic.  WHAM doesn't do anything to change this.
> 
>> I want to do a similar thing by applying restraint force on the organic
>> molecule on the bulk water in order to inhibit their movement inside the
>> bulk. Should I consider the removing of the restraint in PMF?
>> 
> 
> In the case of freely diffusing molecules, I suspect such a restraint would 
> have a much more profound impact.  Why do you want to do this?
> 
> -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
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
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Re: [gmx-users] Umbrella sampling tutorial

[Justin Lemkul]

On 10/7/16 4:41 AM, gozde ergin wrote:

Dear all,

I would like to ask a question about Justin’s tutorial. By using the
POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
effect of this restraint removed during the WHAM?



Not to my knowledge, no.  The restraints in the tutorial are there to mimic the 
fact that there are only five peptides, when in reality, there are millions, so 
the effects of the forces are quite different in vitro/in vivo.  Restraining one 
peptide makes the remaining four peptides more stable, more realistic.  WHAM 
doesn't do anything to change this.



I want to do a similar thing by applying restraint force on the organic
molecule on the bulk water in order to inhibit their movement inside the
bulk. Should I consider the removing of the restraint in PMF?



In the case of freely diffusing molecules, I suspect such a restraint would have 
a much more profound impact.  Why do you want to do this?


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

[Justin Lemkul]

On 6/7/16 3:13 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
missing. I am new to gromacs . So please help me out.



That means the gmx distance commands failed.  Run one interactively to see what 
error you get.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

Hi, Justin

I am working with a triple helix using umbrella sampling method. When 
generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15 
configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro 
conf15.gro conf17.gro conf18.gro conf30.gro conf31.gro conf39.gro conf59.gro 
conf87.gro conf161.gro conf233.gro conf360.gro conf488.gro. Most of the 
configurations are within 0-100 frames. Does this affect the umbrella sampling 
simulations? Is there any pulling time requirement when generating the 
configurations?  I was supposed to have a try and find the result, but found 
that the calculation is time-consuming. So I decided to ask you finally.

Thanks a lot,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, 18 March 2015 9:45 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/17/15 9:06 PM, Ming Tang wrote:
 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?

Absolute restraints can be used in the pull code, but I've never done it.  Note 
that such an approach is incompatible with NPT.  Freezing may also be an 
option, but then you're acting directly on all the atoms and frozen groups 
carry their own artificiality.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 4/7/15 7:11 AM, Ming Tang wrote:

Hi, Justin

I am working with a triple helix using umbrella sampling method. When
generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15
configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro
conf15.gro conf17.gro conf18.gro conf30.gro conf31.gro conf39.gro conf59.gro
conf87.gro conf161.gro conf233.gro conf360.gro conf488.gro. Most of the
configurations are within 0-100 frames. Does this affect the umbrella
sampling simulations? Is there any pulling time requirement when generating
the configurations?  I was supposed to have a try and find the result, but
found that the calculation is time-consuming. So I decided to ask you
finally.



The physics of every system is different.  It's hard to generalize.  If you have 
configurations that allow for reasonable window spacing, the quality of the end 
result depends on the sampling and convergence of the umbrella sampling itself.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/17/15 9:06 PM, Ming Tang wrote:

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?


Absolute restraints can be used in the pull code, but I've never done it.  Note 
that such an approach is incompatible with NPT.  Freezing may also be an option, 
but then you're acting directly on all the atoms and frozen groups carry their 
own artificiality.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

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-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http

Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

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.
Could you help to figure out this problem?
Regards,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http

Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

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-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Wednesday, 18 March 2015 10:34 AM
To: gmx-us...@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@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-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Ming Tang
 Sent: Wednesday, 18 March 2015 8:14 AM
 To: gmx-us...@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 jalem...@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-boun...@maillist.sys.kth.se
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Justin Lemkul
 Sent: Monday, 16 March 2015 9:27 PM
 To: gmx-us...@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

Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

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 jalem...@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-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
 Justin Lemkul
 Sent: Monday, 16 March 2015 9:27 PM
 To: gmx-us...@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

Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

Hi Justin,

Here is the error message.
tm@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.

Thanks,
Ming
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Wednesday, 18 March 2015 8:14 AM
To: gmx-us...@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 jalem...@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-boun...@maillist.sys.kth.se 
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf 
 Of Justin Lemkul
 Sent: Monday, 16 March 2015 9:27 PM
 To: gmx-us...@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

Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/17/15 8:08 PM, Ming Tang wrote:

Hi Justin,

Here is the error message.
tm@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-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Wednesday, 18 March 2015 8:14 AM
To: gmx-us...@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 jalem...@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-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf
Of Justin Lemkul
Sent: Monday, 16 March 2015 9:27 PM
To: gmx-us...@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

Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

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.
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.

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?  

Thanks,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Friday, 13 March 2015 10:57 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/12/15 8:49 PM, Ming Tang wrote:
 Dear Justin,

 I switched Chain_A and Chain_B in the .mdp file, but got the same result.
 In the tutorial:
 pull-ngroups: (1)
 The number of pull groups, not including the absolute reference group, when 
 used. And we need to assign the Chain_B as the reference group.


So does this mean things are working if you set pull-ngroups = 1 (which it 
should have been)?

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

Dear Justin,

The results turned out that the COM distance between them is the same over 
time, seems that both Chain_A and Chain_B had been pulled by the same force in 
the same direction, which is different from the tutorial.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Thursday, 12 March 2015 11:34 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial

Hi Justin,

Your code works!
Thank you very much.

Regards,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 12 March 2015 11:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/11/15 8:58 PM, Ming Tang wrote:
 Dear Justin,

 Thanks for your help.
 I changed the group names to Chain_A and Chain_B in my index file, and 
 modified the COM pulling code.

 ; COM pulling
 pull= umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim= N N Y
 pull_start  = yes   ; define initial COM distance  0
 pull-ngroups= 1
 ?assign the reference group?
 pull-group1-name= Chain_A
 pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
 pull-coord1-k = 1000  ; kJ mol^-1 nm^-2

 But I didn't found the order to assign the reference group Chain_B in 
 GROMACS 5.0.4 Could you give me some help?


Something like this (I haven't tested it, so please let me know if this 
works...or doesn't):

pull= umbrella
pull-geometry   = distance
pull-dim= N N Y
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= Chain_A
pull-group2-name= Chain_B
pull-coord1-rate= 0.01
pull-coord1-k   = 1000

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Nima Soltani]

 On 3/11/15 4:17 AM, Ming Tang wrote:
  Dear all,
 
  I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
  Everything was fine until I got to the step five (run the continuous
pulling simulation).
  Then I turned to the 5.0.4 manual, and tried to modify the pull code,
but failed.
 
  ; Pull code in tutorial
  pull= umbrella
  pull_geometry   = distance  ; simple distance increase
  pull_dim= N N Y
  pull_start  = yes   ; define initial COM distance  0
  pull_ngroups= 1
  pull_group0 = Chain_B
  pull_group1 = Chain_A
  pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
  pull_k1 = 1000  ; kJ mol^-1 nm^-2
 
  ; COM pulling I modified
  pull= umbrella
  pull_geometry= distance  ; simple distance increase
  pull_dim = N N Y
  pull_start   = yes   ; define initial COM distance  0
  pull_coord1-groups   = 2

Group 1  2  participating in reaction coordinate So it is wrong to state
just group 2 in pull_coord1-groups   = 2
change it to : pull_coord1_groups= 1 2 

  pull-group1-name = Chain_B
  pull_group2-name = Chain_A
  pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
  pull-coord1-k= 1000  ; kJ mol^-1 nm^-2
 
  Fatal error:
  Group Chain_B referenced in the .mdp file was not found in the index file.
  Group names must match either [moleculetype] names or custom index group
  names, in which case you must supply an index file to the '-n' option
  of grompp.
 
  Could anybody tell me what's wrong with the COM pulling code I modified?
 
Best Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=



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Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

Dear Justin,

I switched Chain_A and Chain_B in the .mdp file, but got the same result. 
In the tutorial:
pull-ngroups: (1)
The number of pull groups, not including the absolute reference group, when 
used. And we need to assign the Chain_B as the reference group.

Thanks,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 12 March 2015 9:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/12/15 2:41 AM, Ming Tang wrote:

 Dear Justin,

 The results turned out that the COM distance between them is the same over 
 time, seems that both Chain_A and Chain_B had been pulled by the same force 
 in the same direction, which is different from the tutorial.


Switch Chain_A and Chain_B in the .mdp file.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/12/15 8:49 PM, Ming Tang wrote:

Dear Justin,

I switched Chain_A and Chain_B in the .mdp file, but got the same result.
In the tutorial:
pull-ngroups: (1)
The number of pull groups, not including the absolute reference group, when 
used. And we need to assign the Chain_B as the reference group.



So does this mean things are working if you set pull-ngroups = 1 (which it 
should have been)?


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/12/15 2:41 AM, Ming Tang wrote:


Dear Justin,

The results turned out that the COM distance between them is the same over 
time, seems that both Chain_A and Chain_B had been pulled by the same force in 
the same direction, which is different from the tutorial.



Switch Chain_A and Chain_B in the .mdp file.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/11/15 8:58 PM, Ming Tang wrote:

Dear Justin,

Thanks for your help.
I changed the group names to Chain_A and Chain_B in my index file, and modified 
the COM pulling code.

; COM pulling
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance  0
pull-ngroups= 1
?assign the reference group?
pull-group1-name= Chain_A
pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k = 1000  ; kJ mol^-1 nm^-2

But I didn't found the order to assign the reference group Chain_B in GROMACS 
5.0.4
Could you give me some help?



Something like this (I haven't tested it, so please let me know if this 
works...or doesn't):


pull= umbrella
pull-geometry   = distance
pull-dim= N N Y
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= Chain_A
pull-group2-name= Chain_B
pull-coord1-rate= 0.01
pull-coord1-k   = 1000

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/11/15 4:17 AM, Ming Tang wrote:

Dear all,

I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
Everything was fine until I got to the step five (run the continuous pulling 
simulation).
Then I turned to the 5.0.4 manual, and tried to modify the pull code, but 
failed.

; Pull code in tutorial
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 1
pull_group0 = Chain_B
pull_group1 = Chain_A
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2

; COM pulling I modified
pull= umbrella
pull_geometry= distance  ; simple distance increase
pull_dim = N N Y
pull_start   = yes   ; define initial COM distance  0
pull_coord1-groups   = 2
pull-group1-name = Chain_B
pull_group2-name = Chain_A
pull-coord1-rate = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k= 1000  ; kJ mol^-1 nm^-2

Fatal error:
Group Chain_B referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

Index:
[ r_1-27 ]
123456789   10   11   12   13   14   15
   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135
  136  137  138  139  140  141  142  143  144  145  146  147  148  149  150
  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165
  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180
  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195
  196  197  198  199  200  201  202  203  204  205  206  207  208  209  210
  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225
  226
[ r_28-54 ]
227  228  229  230  231  232  233  234  235  236  237  238  239  240  241
  242  243  244  245  246  247  248  249  250  251  252  253  254  255  256
  257  258  259  260  261  262  263  264  265  266  267  268  269  270  271
  272  273  274  275  276  277  278  279  280  281  282  283  284  285  286
  287  288  289  290  291  292  293  294  295  296  297  298  299  300  301
  302  303  304  305  306  307  308  309  310  311  312  313  314  315  316
  317  318  319  320  321  322  323  324  325  326  327  328  329  330  331
  332  333  334  335  336  337  338  339  340  341  342  343  344  345  346
  347  348  349  350  351  352  353  354  355  356  357  358  359  360  361
  362  363  364  365  366  367  368  369  370  371  372  373  374  375  376
  377  378  379  380  381  382  383  384  385  386  387  388  389  390  391
  392  393  394  395  396  397  398  399  400  401  402  403  404  405  406
  407  408  409  410  411  412  413  414  415  416  417  418  419  420  421
  422  423  424  425  426  427  428  429  430  431  432  433  434  435  436
  437  438  439  440  441  442  443  444  445  446  447  448  449  450  451
  452

Could anybody tell me what's wrong with the COM pulling code I modified?



The groups have not been named Chain_A and Chain_B, but that's how you're 
attempting to use them.  Rename them in the .ndx or .mdp.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] umbrella sampling tutorial

[Ming Tang]

Hi Justin,

Your code works!
Thank you very much.

Regards,
Ming

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Thursday, 12 March 2015 11:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial



On 3/11/15 8:58 PM, Ming Tang wrote:
 Dear Justin,

 Thanks for your help.
 I changed the group names to Chain_A and Chain_B in my index file, and 
 modified the COM pulling code.

 ; COM pulling
 pull= umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim= N N Y
 pull_start  = yes   ; define initial COM distance  0
 pull-ngroups= 1
 ?assign the reference group?
 pull-group1-name= Chain_A
 pull-coord1-rate  = 0.01  ; 0.01 nm per ps = 10 nm per ns
 pull-coord1-k = 1000  ; kJ mol^-1 nm^-2

 But I didn't found the order to assign the reference group Chain_B in 
 GROMACS 5.0.4 Could you give me some help?


Something like this (I haven't tested it, so please let me know if this 
works...or doesn't):

pull= umbrella
pull-geometry   = distance
pull-dim= N N Y
pull-start  = yes
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= Chain_A
pull-group2-name= Chain_B
pull-coord1-rate= 0.01
pull-coord1-k   = 1000

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Umbrella Sampling Tutorial Question

[Justin Lemkul]

On 10/31/14 8:48 PM, Agnivo Gosai wrote:

Dear Users

Firstly thanks to Dr. Lemkul for his immensely informative and helpful
tutorials. I am following the umbrella sampling tutorial for one of my
projects.
During the placement of the molecule inside the box , the tutorial tells us
to visualize in VMD. Now , upon visualizing I find that the 4 strands of
protofibril protein look separated.
Then we are to restrain one of the strands and pull the next stand in the
pulling simulation.
I can not understand how this is physically possible as the strands
appear to be physically separated and we proceed to calculate PMF based
on binding energy.

Kindly shed some light on this issue , please. Pardon for my ignorance.



The strands shouldn't be separated.  The input .pdb file is a pentamer.  The 
commands in the tutorial won't modify the coordinates.  If you're seeing 
something significantly different from the image in the tutorial, start over and 
don't do anything that isn't explicitly stated in the tutorial.  If you're still 
having issues, you're going to have to link an image so we can see what is going 
on.  The phrase look separated isn't very descriptive.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Umbrella Sampling Tutorial

[Justin Lemkul]

On 1/11/14, 11:50 AM, Andres Ortega wrote:

Hi,

Dear Gromacs Users

I was running de Umbrella Sampling Tutorial, and when i get the frames from
the trajectory, there are some frames like this:

489 5.3776196
490 5.3817739
491 5.3752654
492 5.3619911
493 5.3890083
494 5.3918220
495 5.4115819
496 5.4074620
497 5.4386061
498 5.4179682
499 5.3942749
500 5.3905423

is this ok? , they shouldn´t be always move away from the other molecule ?



This is perfectly fine.  At this COM distance, there is no appreciable 
interaction between the reference and pulled groups, so the pulled group mostly 
just diffuses randomly at this point.  Remember that the spring is pulled with 
constant velocity, but the pulled species only responds to both this applied 
force and the forces within the system, which at this point are just collisions 
with the solvent.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 12/1/13 8:04 AM, shahab shariati wrote:

Dear Justin

Very thanks for your reply

I will slow pulling by changing pull_rate1 from 0.01 to 0.001
and pull_k1 from 1000 to 100.

I have a basic question. Before minimization, where should I put drug
molecule? into water molecules or into lipid bilayer? Should I put drug
molecule in the specific position?



If you're trying to pull it into/across the bilayer, the most intuitive thing to 
do is place it within the water and pull it across to set up your 
configurations.  You can do it however you like.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 12/1/13 10:38 AM, shahab shariati wrote:

Dear Justin

When I placed drug within the lipid bilayer, after Generating Configurations
step, I obtained 501 gro files. When I used distance.pl script for these
gro files, my summary_distances.dat file is as follows:

00.2756352
10.2535359
20.2447009
30.3004653
40.2936225
50.1910549
60.2493761
70.2033079
80.1769952
90.2731782
100.2927040
110.3717106
120.3232497
.
.
.
.
4850.7589852
4860.6876000
4870.6966222
4880.7487700
4890.7043532
4900.6424745
4910.7194880
4920.6209456
4930.6327312
4940.6861565
4950.5513341
4960.6917742
4970.7074009
4980.7403648
4990.6833771
5000.7035147

As can be seen the range of distance is 0.27-0.7, while the dimensions of
box is  5.92819   6.43131   7.75764.

My supposition was that the range of distance should be 0-3.9 (7.75764/2).

You are right. The settings depend on where I place everything.
This is my first experience in com pulling. Please guide me to use
appropriate Pull code parameters in my case (drug molecules within the
lipid bilayer).

I used following Pull code parameters:

; Pull code
pull= umbrella
pull_geometry   = position  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 1
pull_group0 = CHOL_DOPC
pull_group1 = drg
pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 100  ; kJ mol^-1 nm^-2
pull_init1  = 0
pull_vec1   = 0 0 1

Except Pull code parameters, what things are important?



I have never attempted such a pulling procedure.  Hopefully someone else will 
comment on their experiences.  Do not try to hack the tutorial into working for 
your system; the approaches will be quite different.  The manual explains the 
logic behind the different geometries; you may have to experiment a bit to get 
things to work.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Umbrella Sampling tutorial

[Dr. Vitaly Chaban]

The output you got indicates that the pulled group came to the
location where it is expected by gromacs to be.

The input looks correct, but gromacs' pull code is with surprise
inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0
0 1. Turning off barostat during pulling also saves nerves.

It must be possible to pull through the whole box, not up to the
middle of Z side.

Dr. Vitaly V. Chaban


On Sun, Dec 1, 2013 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 12/1/13 10:38 AM, shahab shariati wrote:

 Dear Justin

 When I placed drug within the lipid bilayer, after Generating
 Configurations
 step, I obtained 501 gro files. When I used distance.pl script for these
 gro files, my summary_distances.dat file is as follows:

 00.2756352
 10.2535359
 20.2447009
 30.3004653
 40.2936225
 50.1910549
 60.2493761
 70.2033079
 80.1769952
 90.2731782
 100.2927040
 110.3717106
 120.3232497
 .
 .
 .
 .
 4850.7589852
 4860.6876000
 4870.6966222
 4880.7487700
 4890.7043532
 4900.6424745
 4910.7194880
 4920.6209456
 4930.6327312
 4940.6861565
 4950.5513341
 4960.6917742
 4970.7074009
 4980.7403648
 4990.6833771
 5000.7035147

 As can be seen the range of distance is 0.27-0.7, while the dimensions of
 box is  5.92819   6.43131   7.75764.

 My supposition was that the range of distance should be 0-3.9 (7.75764/2).

 You are right. The settings depend on where I place everything.
 This is my first experience in com pulling. Please guide me to use
 appropriate Pull code parameters in my case (drug molecules within the
 lipid bilayer).

 I used following Pull code parameters:

 ; Pull code
 pull= umbrella
 pull_geometry   = position  ; simple distance increase
 pull_dim= N N Y
 pull_start  = yes   ; define initial COM distance  0
 pull_ngroups= 1
 pull_group0 = CHOL_DOPC
 pull_group1 = drg
 pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
 pull_k1 = 100  ; kJ mol^-1 nm^-2
 pull_init1  = 0
 pull_vec1   = 0 0 1

 Except Pull code parameters, what things are important?


 I have never attempted such a pulling procedure.  Hopefully someone else
 will comment on their experiences.  Do not try to hack the tutorial into
 working for your system; the approaches will be quite different.  The manual
 explains the logic behind the different geometries; you may have to
 experiment a bit to get things to work.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/30/13 9:22 AM, shahab shariati wrote:

Dear Justin

My system contains lipid bilayer + drug + water molecules.

I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.

Based on your suggestion I used pull_geometry = position for my case.

After the minimization and equilibration, for Generating Configurations
step, I used following parameters in the md-pull.mdp file:
--
title   = md-pull
; Run parameters
integrator   = md
nsteps   = 50
dt = 0.002
; Output control
nstxout  = 1000
nstvout  = 1000
nstxtcout   = 1000
nstenergy   = 1000
nstlog= 1000
energygrps  = CHOL DOPC drg SOL
; Bond parameters
continuation= yes
constraint_algorithm = lincs
constraints  = all-bonds
lincs_iter = 1
lincs_order  = 4
; Neighborsearching
ns_type  = grid
nstlist= 5
rlist= 1.0
rcoulomb = 1.0
rvdw   = 1.0
; Electrostatics
coulombtype= PME
pme_order   = 4
fourierspacing   = 0.16
; Temperature coupling is on
tcoupl = V-rescale
tc-grps= CHOL_DOPCdrg SOL
tau_t  = 0.50.5   0.5
ref_t   = 323 323   323
; Pressure coupling is on
pcoupl = Berendsen
pcoupltype   = semiisotropic
tau_p  = 2.0
ref_p   = 1.01.0
compressibility   = 4.5e-54.5e-5
; Periodic boundary conditions
pbc  = xyz
; Dispersion correction
DispCorr   = EnerPres
; Velocity generation
gen_vel = no
; COM motion removal
nstcomm   = 1
comm-mode   = Linear
comm-grps= CHOL_DOPC_drg  SOL
; Pull code
pull  = umbrella
pull_geometry= position
pull_dim= N N Y
pull_start  = yes
pull_ngroups  = 1
pull_group0= CHOL_DOPC
pull_group1= drg
pull_rate1  = 0.01
pull_k1  = 1000
pull_init1   = 0
pull_vec1   = 0 0 1
-

Then I used following tools:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
pull.tpr
mdrun -s pull.tpr

pull.gro file was not created and there are strange pdb files with names:

step240702b_n0.pdb
step240702c_n0.pdb
step240704b_n0.pdb
step240704c_n0.pdb
step240706b_n0.pdb
step240706c_n0.pdb
step240707b_n0.pdb
step240707c_n0.pdb
step240708b_n0.pdb
step240708c_n0.pdb
step240709b_n0.pdb
step240709b_n1.pdb
step240709c_n0.pdb
step240709c_n1.pdb

While, there should be obtained 500 frames. I saw one of these pdb files by
VMD,
(step240708c_n0.pdb). I attached figure related to this pdb in below link:

https://www.dropbox.com/s/6qnn4okv63qieec/pdb%20file.docx

When I use trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep, only 241 gro
files
were created from conf0.gro to conf240.gro instead of 501 gro files.

I used same parameters in mdp file except Pull code parameters
for simulation of my system for 20 ns and there are no problems.

What is the reason of this state? Is my Pull code parameters wrong?



Applying the pulling restraint is causing the system to crash halfway through 
the simulation.  There is nothing immediately obvious to me about why it is 
happening.  Check out 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. 
 Try slower pulling or a weaker force constant.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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