Re: [gmx-users] virtual sites for ligands?

[Mark Abraham]

Hi,

No, you'll have to build such a topology yourself

Mark

On Fri., 12 Jul. 2019, 19:21 Carlos Navarro, 
wrote:

> Dear gmx-users,
> Is there a way to create a vsite-H topology of a ligand using gromacs
> (pdb2gmx)?
> Best regards,
> Carlos
>
> ——
> Carlos Navarro Retamal
> Bioinformatic Engineering. PhD.
> Postdoctoral Researcher in Center of Bioinformatics and Molecular
> Simulations
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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[gmx-users] virtual sites for ligands?

[Carlos Navarro]

Dear gmx-users,
Is there a way to create a vsite-H topology of a ligand using gromacs
(pdb2gmx)?
Best regards,
Carlos

——
Carlos Navarro Retamal
Bioinformatic Engineering. PhD.
Postdoctoral Researcher in Center of Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
-- 
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-requ...@gromacs.org.

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 6/6/18 11:13 AM, Eisenhart, Andrew (eisenhaw) wrote:

new link with sole mdp file

https://files.fm/u/cmyg863c


This system doesn't even survive energy minimization for me, suggesting 
that the topology is not stable. The machine I'm on uses GROMACS 2016.3. 
Please upgrade to at least that version, if not 2018.1, because 5.1.2 is 
not even the terminal version in that series.


Your topology specifies a SETTLE geometry for an SPC-like water, which 
immediately leads to each of your waters (which have O-H distances of 
0.181 nm and H-H of 0.286 nm) to shrink inward, also shifting your 
virtual sites. That minimization simply crashes. I changed the SETTLE 
geometry to agree with your initial geometry, and while the atomic sites 
are OK, the qh1 and qh2 virtual sites expand outward, and though EM 
finishes, the max force is on the order of 10^8.


Check your virtual site construction, as this may be the source of the 
buildup in force. Use "nstxout = 1" in your em.mdp to see this happening 
more clearly.


Your cutoffs are bizarrely short but don't seem to be a problem. Once 
you've sorted out your topology issues, make sure your physical model is 
sane with such tiny cutoffs.


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 9:30 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.

Please use tgz or just upload a plain-text em.mdp.

-Justin


https://files.fm/u/r65e3kzq

[https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq>

2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq>
files.fm
Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP 
alternative. Free signup. Unlimited download traffic via torrents.



Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.


em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin


<https://files.fm/u/c9uef9qh>

https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

new link with sole mdp file

https://files.fm/u/cmyg863c


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 9:30 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:
> Sorry about that, he’s a another link to the same files with the fixed 
> em.mdp. I hope the 7zip format is ok.

Please use tgz or just upload a plain-text em.mdp.

-Justin

> https://files.fm/u/r65e3kzq
[https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq>

2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq>
files.fm
Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP 
alternative. Free signup. Unlimited download traffic via torrents.


>
> Andrew E. Eisenhart
> Graduate Research Assistant | University of Cincinnati
> 330.383.5061
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: Tuesday, June 5, 2018 7:05:51 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
>
>
> On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:
>> Here's the link to the files, if there's anything else I can send let me 
>> know. I've been using 5.1.1 for the initial set up and energy minimization, 
>> and 5.1.2 for the nvt and npt simulations.
>>
> em.mdp is some corrupted binary file. Please upload a corrected version.
>
> -Justin
>
>> <https://files.fm/u/c9uef9qh>
>>
>> https://files.fm/u/c9uef9qh
>>
>>
>>
>> Thanks
>>
>> Andrew
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Justin 
>> Lemkul 
>> Sent: Tuesday, June 5, 2018 12:54:50 PM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>
>>
>>
>> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
>>> Hello again,
>>>
>>> I have done a few things since I last updated this list.
>>>
>>>
>>> I generated a new system of only 1000 water instead of the original 2000, I 
>>> used a more careful approach in my energy minimization, minimizing first 
>>> with all bonds and angles constrained then again without those hash 
>>> constraints. This succeeded in getting the maximum force in my system to 
>>> below 100kcal without lincs warnings.
>>>
>>>
>>> Then I proceeded to equilibrate the temperature as before with no issues, 
>>> and finally I attempted to equilibrate the box size  using the Berendsen 
>>> barostat running for 2ns. The box size increases as before and still does 
>>> not converge. The system stays at around 300K, but after a while (~1ns) it 
>>> seems to fill the box like its a gas visually at least.
>>>
>>> So any ideas that I could try would be appreciated.
>> If you can assemble a tarball that contains starting coordinates (not
>> minimized), topology, all .mdp files, and a run script that gives the
>> exact sequence of what you're doing, and post it somewhere to share, I
>> will try to take a look at it and see if I can reproduce the behavior.
>>
>> What version of GROMACS are you using?
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Andrew
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>>  on behalf of Eisenhart, 
>>> Andrew (eisenhaw) 
>>> Sent: Thursday, May 31, 2018 1:51:51 PM
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>>
>>> Hey,
>>>
>>> Thanks for everyone's response.
>>>
>>>
>>> I have tried using the berendsen barostat, with it I see similar behavior 
>>> with the unit cell jumping up in size and then steadily increasing in size. 
>>> I have some longer runs using it running now (2-3ns), so I'll be able to 
>>> see it it eventually converges.
>>>
>>>
>>> Nice catch with the particle type being incorrect, but with it corrected 
>>> I'm still having the same problems (ie the oscillation of the box size) it 
>>> has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
>>> simulate for a longer amount of time to see if it will converge.
>>>
>>>
>>

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.


Please use tgz or just upload a plain-text em.mdp.

-Justin


https://files.fm/u/r65e3kzq

Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.


em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin


<https://files.fm/u/c9uef9qh>

https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
 qm1   qm1 0.000   -2.516V  0.000  0.000
 qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2  

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.

https://files.fm/u/r65e3kzq

Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:
> Here's the link to the files, if there's anything else I can send let me 
> know. I've been using 5.1.1 for the initial set up and energy minimization, 
> and 5.1.2 for the nvt and npt simulations.
>

em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin

> <https://files.fm/u/c9uef9qh>
>
> https://files.fm/u/c9uef9qh
>
>
>
> Thanks
>
> Andrew
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: Tuesday, June 5, 2018 12:54:50 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
>
>
> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
>> Hello again,
>>
>> I have done a few things since I last updated this list.
>>
>>
>> I generated a new system of only 1000 water instead of the original 2000, I 
>> used a more careful approach in my energy minimization, minimizing first 
>> with all bonds and angles constrained then again without those hash 
>> constraints. This succeeded in getting the maximum force in my system to 
>> below 100kcal without lincs warnings.
>>
>>
>> Then I proceeded to equilibrate the temperature as before with no issues, 
>> and finally I attempted to equilibrate the box size  using the Berendsen 
>> barostat running for 2ns. The box size increases as before and still does 
>> not converge. The system stays at around 300K, but after a while (~1ns) it 
>> seems to fill the box like its a gas visually at least.
>>
>> So any ideas that I could try would be appreciated.
> If you can assemble a tarball that contains starting coordinates (not
> minimized), topology, all .mdp files, and a run script that gives the
> exact sequence of what you're doing, and post it somewhere to share, I
> will try to take a look at it and see if I can reproduce the behavior.
>
> What version of GROMACS are you using?
>
> -Justin
>
>> Thanks,
>>
>> Andrew
>>
>> ____
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Eisenhart, 
>> Andrew (eisenhaw) 
>> Sent: Thursday, May 31, 2018 1:51:51 PM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>
>> Hey,
>>
>> Thanks for everyone's response.
>>
>>
>> I have tried using the berendsen barostat, with it I see similar behavior 
>> with the unit cell jumping up in size and then steadily increasing in size. 
>> I have some longer runs using it running now (2-3ns), so I'll be able to see 
>> it it eventually converges.
>>
>>
>> Nice catch with the particle type being incorrect, but with it corrected I'm 
>> still having the same problems (ie the oscillation of the box size) it has 
>> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
>> simulate for a longer amount of time to see if it will converge.
>>
>>
>> Thanks again for everyone's reply, below is my .itp in its entirety maybe 
>> there is an error in the exceptions(which im still not 100% sure about) or 
>> something else that will stand out.
>>
>>
>> Andrew
>>
>>
>> ;
>>
>> [ atomtypes ]
>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>> qm1   qm1 0.000   -2.516V  0.000  0.000
>> qh1   qh1 0.0001.258V  0.000  0.000
>>
>> [ moleculetype ]
>> ; molname   nrexcl
>> M3  3
>>
>> [ atoms ]
>> ; idat type res nr  residu name at name cg nr   charge
>> 1   opls_1131   M3  OW 1   0.0
>> 2   opls_1141   M3 HW1 1   0.0
>> 3   opls_1141   M3 HW2 1   0.0
>> 4   qm1 1   M3  qm 1  -2.516
>> 5   qh1 1   M3 qh1 1   1.258
>> 6   qh1 1   M3 qh2 1   1.258
&

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.



em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin


<https://files.fm/u/c9uef9qh>

https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
qm1   qm1 0.000   -2.516V  0.000  0.000
qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:


On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:

Hello all,

I am having an issue with the current system

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.


<https://files.fm/u/c9uef9qh>

https://files.fm/u/c9uef9qh



Thanks

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
> Hello again,
>
> I have done a few things since I last updated this list.
>
>
> I generated a new system of only 1000 water instead of the original 2000, I 
> used a more careful approach in my energy minimization, minimizing first with 
> all bonds and angles constrained then again without those hash constraints. 
> This succeeded in getting the maximum force in my system to below 100kcal 
> without lincs warnings.
>
>
> Then I proceeded to equilibrate the temperature as before with no issues, and 
> finally I attempted to equilibrate the box size  using the Berendsen barostat 
> running for 2ns. The box size increases as before and still does not 
> converge. The system stays at around 300K, but after a while (~1ns) it seems 
> to fill the box like its a gas visually at least.
>
> So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin

> Thanks,
>
> Andrew
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Eisenhart, 
> Andrew (eisenhaw) 
> Sent: Thursday, May 31, 2018 1:51:51 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
> Hey,
>
> Thanks for everyone's response.
>
>
> I have tried using the berendsen barostat, with it I see similar behavior 
> with the unit cell jumping up in size and then steadily increasing in size. I 
> have some longer runs using it running now (2-3ns), so I'll be able to see it 
> it eventually converges.
>
>
> Nice catch with the particle type being incorrect, but with it corrected I'm 
> still having the same problems (ie the oscillation of the box size) it has 
> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
> simulate for a longer amount of time to see if it will converge.
>
>
> Thanks again for everyone's reply, below is my .itp in its entirety maybe 
> there is an error in the exceptions(which im still not 100% sure about) or 
> something else that will stand out.
>
>
> Andrew
>
>
> ;
>
> [ atomtypes ]
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>qm1   qm1 0.000   -2.516V  0.000  0.000
>qh1   qh1 0.0001.258V  0.000  0.000
>
> [ moleculetype ]
> ; molname   nrexcl
> M3  3
>
> [ atoms ]
> ; idat type res nr  residu name at name cg nr   charge
> 1   opls_1131   M3  OW 1   0.0
> 2   opls_1141   M3 HW1 1   0.0
> 3   opls_1141   M3 HW2 1   0.0
> 4   qm1 1   M3  qm 1  -2.516
> 5   qh1 1   M3 qh1 1   1.258
> 6   qh1 1   M3 qh2 1   1.258
> #ifndef FLEXIBLE
>
> [ settles ]
> ; OWfunct   dohdhh
> 1   1   0.095720.15139
> #else
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 502416.0 0.09572502416.0
> 1   3   1   0.09572 502416.0 0.09572502416.0
>
> [ angles ]
> ; i j   k   funct   angle   force.c.
> 2   1   3   1   104.52  628.02  104.52  628.02
> #endif
>
> [ exclusions ]
> 1   2   3   4   5   6
> 2   1   3   4   5   6
> 3   1   2   4   5   6
> 4   1   2   3   5   6
> 5   1   2   3   4   6
> 6   1   2   3   4   5
>
> [ virtual_sites3 ]
> ; Vsite fromfunct   a   b
> 4   1   2   3   1   0.29869481802   0.29869481802
> ; Vsite (3fad) funct        theta   d
> 5   3   2   1   3 18.060.025
> 6   2   3   1   3 18.060.025
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Mark Abraham 
> 
> Sent: Thursday, May 31, 2018 7:54:09 AM
> To: gmx-us...@gromacs.org
> Sub

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.


If you can assemble a tarball that contains starting coordinates (not 
minimized), topology, all .mdp files, and a run script that gives the 
exact sequence of what you're doing, and post it somewhere to share, I 
will try to take a look at it and see if I can reproduce the behavior.


What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
   qm1   qm1 0.000   -2.516V  0.000  0.000
   qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:



On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:

Hello all,

I am having an issue with the current systems I am working on. The

system consists of 2000 6point water molecules (3 chargeless masses for Ow,
hw1, and hw2; and 3 massless point charges for the electrostatics). The
three point charges I have implemented as virtual interaction sites using
the section below in my topology file.


[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025


this is loosely based on the tip4p model. Since the two partial charges

off of the hydrogens differ only in location I have them defined as a
single type with sigma

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, 
Andrew (eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
  qm1   qm1 0.000   -2.516V  0.000  0.000
  qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:

>
>
> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:
> > Hello all,
> >
> > I am having an issue with the current systems I am working on. The
> system consists of 2000 6point water molecules (3 chargeless masses for Ow,
> hw1, and hw2; and 3 massless point charges for the electrostatics). The
> three point charges I have implemented as virtual interaction sites using
> the section below in my topology file.
> >
> >
> > [ virtual_sites3 ]
> > ; Vsite fromfunct   a   b
> > 4   1   2   3   1   0.29869481802   0.29869481802
> > ; Vsite (3fad) functtheta   d
> > 5   3   2   1   3 18.060.025
> > 6   2   3   1   3 18.060.025
> >
> >
> > this is loosely based on the tip4p model. Since the two partial charges
> off of the hydrogens differ only in location I have them defined as a
> single type with sigma and epsilon defined as 0. I have also done this to
> the partial charge off of the oxygen. This is all seen below in my
> atomtypes and atoms sections.
> >
> >
> > [ atomtypes ]
> > ; nam

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for 
a longer amount of time to see if it will converge.


Thanks again for everyone's reply, below is my .itp in its entirety maybe there 
is an error in the exceptions(which im still not 100% sure about) or something 
else that will stand out.


Andrew


;

[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
  qm1   qm1 0.000   -2.516V  0.000  0.000
  qh1   qh1 0.0001.258V  0.000  0.000

[ moleculetype ]
; molname   nrexcl
M3  3

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258
#ifndef FLEXIBLE

[ settles ]
; OWfunct   dohdhh
1   1   0.095720.15139
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.52  628.02  104.52  628.02
#endif

[ exclusions ]
1   2   3   4   5   6
2   1   3   4   5   6
3   1   2   4   5   6
4   1   2   3   5   6
5   1   2   3   4   6
6   1   2   3   4   5

[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, May 31, 2018 7:54:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:

>
>
> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:
> > Hello all,
> >
> > I am having an issue with the current systems I am working on. The
> system consists of 2000 6point water molecules (3 chargeless masses for Ow,
> hw1, and hw2; and 3 massless point charges for the electrostatics). The
> three point charges I have implemented as virtual interaction sites using
> the section below in my topology file.
> >
> >
> > [ virtual_sites3 ]
> > ; Vsite fromfunct   a   b
> > 4   1   2   3   1   0.29869481802   0.29869481802
> > ; Vsite (3fad) functtheta   d
> > 5   3   2   1   3 18.060.025
> > 6   2   3   1   3 18.060.025
> >
> >
> > this is loosely based on the tip4p model. Since the two partial charges
> off of the hydrogens differ only in location I have them defined as a
> single type with sigma and epsilon defined as 0. I have also done this to
> the partial charge off of the oxygen. This is all seen below in my
> atomtypes and atoms sections.
> >
> >
> > [ atomtypes ]
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >qm1   qm1 0.000   -2.516A  0.000  0.000
> >qh1   qh1 0.0001.258A  0.000  0.000
>
> The particle type for these should be V. This could be the problem - if
> you've encoded an incorrect particle type then the update routines will
> not propagate them correctly.
>
> -Justin
>
> > ---
> >
> > [ atoms ]
> > ; idat type res nr  residu name at name cg nr   charge
> > 1   opls_1131   M3  OW 1   0.0
> > 2   opls_1141   M3 HW1 1   0.0
> > 3   opls_1141   M3 HW2 1   0.0
> > 4   qm1 1   M3  qm 1  -2.516
> > 5   qh1 1   M3 qh1 1   1.258
> > 6   qh1 1   M3 qh2 1   1.258
> >
> > The problem I am seeing right now depends on the parameters I use in the
> mdp files. D

Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Mark Abraham]

Hi,

If that fixes the issue, then please let us know - we should consider
fixing grompp to check that the inputs have appropriate consistency.

Mark

On Thu, May 31, 2018 at 1:48 PM Justin Lemkul  wrote:

>
>
> On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:
> > Hello all,
> >
> > I am having an issue with the current systems I am working on. The
> system consists of 2000 6point water molecules (3 chargeless masses for Ow,
> hw1, and hw2; and 3 massless point charges for the electrostatics). The
> three point charges I have implemented as virtual interaction sites using
> the section below in my topology file.
> >
> >
> > [ virtual_sites3 ]
> > ; Vsite fromfunct   a   b
> > 4   1   2   3   1   0.29869481802   0.29869481802
> > ; Vsite (3fad) functtheta   d
> > 5   3   2   1   3 18.060.025
> > 6   2   3   1   3 18.060.025
> >
> >
> > this is loosely based on the tip4p model. Since the two partial charges
> off of the hydrogens differ only in location I have them defined as a
> single type with sigma and epsilon defined as 0. I have also done this to
> the partial charge off of the oxygen. This is all seen below in my
> atomtypes and atoms sections.
> >
> >
> > [ atomtypes ]
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >qm1   qm1 0.000   -2.516A  0.000  0.000
> >qh1   qh1 0.0001.258A  0.000  0.000
>
> The particle type for these should be V. This could be the problem - if
> you've encoded an incorrect particle type then the update routines will
> not propagate them correctly.
>
> -Justin
>
> > ---
> >
> > [ atoms ]
> > ; idat type res nr  residu name at name cg nr   charge
> > 1   opls_1131   M3  OW 1   0.0
> > 2   opls_1141   M3 HW1 1   0.0
> > 3   opls_1141   M3 HW2 1   0.0
> > 4   qm1 1   M3  qm 1  -2.516
> > 5   qh1 1   M3 qh1 1   1.258
> > 6   qh1 1   M3 qh2 1   1.258
> >
> > The problem I am seeing right now depends on the parameters I use in the
> mdp files. During thermostat equlibration nothing is amiss, but once the
> volume of the box is allowed to relax the problems show. Using the
> parrinello-rahman barostat and 0.002fs timestep I crash with lincs
> warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but
> the box size never converges It  instead expands to around 10x its original
> size. So I think that I must have a problem with the implementation of my
> virtual sites. Any guidance would be greatly appreciated. Thanks below are
> some other parameters I have set in my input files.
> >
> > Andrew
> >
> >
> > integrator  =  md
> > nsteps  =  50
> > nstcomm =  100
> > nstxout =  0
> > nstvout =  0
> > nstfout =  0
> > nstlog  =  1000
> > nstenergy   =  1000
> > nstxtcout   =  1000
> > nstlist =  5
> > ns_type = grid
> > pbc =  xyz
> > coulombtype = pme
> > rcoulomb= 0.5
> > rlist   = 0.5
> > vdw-type= cut-off
> > rvdw=0.5
> > constraint_algorithm = lincs
> > constraints = all-bonds
> > lincs_iter  = 1
> > lincs_order = 8
> > fourierspacing   = 0.10
> > pme_order= 6
> > ewald_rtol   = 1e-06
> > ewald_geometry   = 3d
> > optimize_fft = yes
> > tcoupl  = Nose-Hoover
> > tc-grps = System
> > tau_t   = 0.4
> > ref_t   = 300
> > ; Pressure coupling is on
> > pcoupl  = parrinello-rahman
> > pcoupltype  = isotropic
> > tau_p   = 2.0
> > ref_p   = 1.0
> > compressibility = 4.5e-5
> > refcoord-scaling = com
> > DispCorr= EnerPres
> > comm-mode   = linear
> >
> >
> >
>
> --
> ==
>
> 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
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote:

Hello all,

I am having an issue with the current systems I am working on. The system 
consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and 
hw2; and 3 massless point charges for the electrostatics). The three point 
charges I have implemented as virtual interaction sites using the section below 
in my topology file.


[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025


this is loosely based on the tip4p model. Since the two partial charges off of 
the hydrogens differ only in location I have them defined as a single type with 
sigma and epsilon defined as 0. I have also done this to the partial charge off 
of the oxygen. This is all seen below in my atomtypes and atoms sections.


[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
   qm1   qm1 0.000   -2.516A  0.000  0.000
   qh1   qh1 0.0001.258A  0.000  0.000


The particle type for these should be V. This could be the problem - if 
you've encoded an incorrect particle type then the update routines will 
not propagate them correctly.


-Justin


---

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258

The problem I am seeing right now depends on the parameters I use in the mdp 
files. During thermostat equlibration nothing is amiss, but once the volume of 
the box is allowed to relax the problems show. Using the parrinello-rahman 
barostat and 0.002fs timestep I crash with lincs warnings. Reducing the 
timestep to 0.001fs stops the lincs warnings, but the box size never converges 
It  instead expands to around 10x its original size. So I think that I must 
have a problem with the implementation of my virtual sites. Any guidance would 
be greatly appreciated. Thanks below are some other parameters I have set in my 
input files.

Andrew


integrator  =  md
nsteps  =  50
nstcomm =  100
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  1000
nstenergy   =  1000
nstxtcout   =  1000
nstlist =  5
ns_type = grid
pbc =  xyz
coulombtype = pme
rcoulomb= 0.5
rlist   = 0.5
vdw-type= cut-off
rvdw=0.5
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter  = 1
lincs_order = 8
fourierspacing   = 0.10
pme_order= 6
ewald_rtol   = 1e-06
ewald_geometry   = 3d
optimize_fft = yes
tcoupl  = Nose-Hoover
tc-grps = System
tau_t   = 0.4
ref_t   = 300
; Pressure coupling is on
pcoupl  = parrinello-rahman
pcoupltype  = isotropic
tau_p   = 2.0
ref_p   = 1.0
compressibility = 4.5e-5
refcoord-scaling = com
DispCorr= EnerPres
comm-mode   = linear





--
==

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] Virtual sites causing npt simulation instabilities

[Dallas Warren]

Always good practice to use Berendsen when turning on constant
pressure first, it is much more robust than P-R.  Let that run for
awhile, let it equilibrate, then turn on P-R.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 31 May 2018 at 06:40, Eisenhart, Andrew (eisenhaw)
 wrote:
> Hello all,
>
> I am having an issue with the current systems I am working on. The system 
> consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and 
> hw2; and 3 massless point charges for the electrostatics). The three point 
> charges I have implemented as virtual interaction sites using the section 
> below in my topology file.
>
>
> [ virtual_sites3 ]
> ; Vsite fromfunct   a   b
> 4   1   2   3   1   0.29869481802   0.29869481802
> ; Vsite (3fad) functtheta   d
> 5   3   2   1   3 18.060.025
> 6   2   3   1   3 18.060.025
>
>
> this is loosely based on the tip4p model. Since the two partial charges off 
> of the hydrogens differ only in location I have them defined as a single type 
> with sigma and epsilon defined as 0. I have also done this to the partial 
> charge off of the oxygen. This is all seen below in my atomtypes and atoms 
> sections.
>
>
> [ atomtypes ]
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>   qm1   qm1 0.000   -2.516A  0.000  0.000
>   qh1   qh1 0.0001.258A  0.000  0.000
>
> ---
>
> [ atoms ]
> ; idat type res nr  residu name at name cg nr   charge
> 1   opls_1131   M3  OW 1   0.0
> 2   opls_1141   M3 HW1 1   0.0
> 3   opls_1141   M3 HW2 1   0.0
> 4   qm1 1   M3  qm 1  -2.516
> 5   qh1 1   M3 qh1 1   1.258
> 6   qh1 1   M3 qh2 1   1.258
>
> The problem I am seeing right now depends on the parameters I use in the mdp 
> files. During thermostat equlibration nothing is amiss, but once the volume 
> of the box is allowed to relax the problems show. Using the parrinello-rahman 
> barostat and 0.002fs timestep I crash with lincs warnings. Reducing the 
> timestep to 0.001fs stops the lincs warnings, but the box size never 
> converges It  instead expands to around 10x its original size. So I think 
> that I must have a problem with the implementation of my virtual sites. Any 
> guidance would be greatly appreciated. Thanks below are some other parameters 
> I have set in my input files.
>
> Andrew
>
>
> integrator  =  md
> nsteps  =  50
> nstcomm =  100
> nstxout =  0
> nstvout =  0
> nstfout =  0
> nstlog  =  1000
> nstenergy   =  1000
> nstxtcout   =  1000
> nstlist =  5
> ns_type = grid
> pbc =  xyz
> coulombtype = pme
> rcoulomb= 0.5
> rlist   = 0.5
> vdw-type= cut-off
> rvdw=0.5
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter  = 1
> lincs_order = 8
> fourierspacing   = 0.10
> pme_order= 6
> ewald_rtol   = 1e-06
> ewald_geometry   = 3d
> optimize_fft = yes
> tcoupl  = Nose-Hoover
> tc-grps = System
> tau_t   = 0.4
> ref_t   = 300
> ; Pressure coupling is on
> pcoupl  = parrinello-rahman
> pcoupltype  = isotropic
> tau_p   = 2.0
> ref_p   = 1.0
> compressibility = 4.5e-5
> refcoord-scaling = com
> DispCorr= EnerPres
> comm-mode   = linear
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

Hello all,

I am having an issue with the current systems I am working on. The system 
consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and 
hw2; and 3 massless point charges for the electrostatics). The three point 
charges I have implemented as virtual interaction sites using the section below 
in my topology file.


[ virtual_sites3 ]
; Vsite fromfunct   a   b
4   1   2   3   1   0.29869481802   0.29869481802
; Vsite (3fad) functtheta   d
5   3   2   1   3 18.060.025
6   2   3   1   3 18.060.025


this is loosely based on the tip4p model. Since the two partial charges off of 
the hydrogens differ only in location I have them defined as a single type with 
sigma and epsilon defined as 0. I have also done this to the partial charge off 
of the oxygen. This is all seen below in my atomtypes and atoms sections.


[ atomtypes ]
; name  bond_typemasscharge   ptype  sigma  epsilon
  qm1   qm1 0.000   -2.516A  0.000  0.000
  qh1   qh1 0.0001.258A  0.000  0.000

---

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   opls_1131   M3  OW 1   0.0
2   opls_1141   M3 HW1 1   0.0
3   opls_1141   M3 HW2 1   0.0
4   qm1 1   M3  qm 1  -2.516
5   qh1 1   M3 qh1 1   1.258
6   qh1 1   M3 qh2 1   1.258

The problem I am seeing right now depends on the parameters I use in the mdp 
files. During thermostat equlibration nothing is amiss, but once the volume of 
the box is allowed to relax the problems show. Using the parrinello-rahman 
barostat and 0.002fs timestep I crash with lincs warnings. Reducing the 
timestep to 0.001fs stops the lincs warnings, but the box size never converges 
It  instead expands to around 10x its original size. So I think that I must 
have a problem with the implementation of my virtual sites. Any guidance would 
be greatly appreciated. Thanks below are some other parameters I have set in my 
input files.

Andrew


integrator  =  md
nsteps  =  50
nstcomm =  100
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  1000
nstenergy   =  1000
nstxtcout   =  1000
nstlist =  5
ns_type = grid
pbc =  xyz
coulombtype = pme
rcoulomb= 0.5
rlist   = 0.5
vdw-type= cut-off
rvdw=0.5
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter  = 1
lincs_order = 8
fourierspacing   = 0.10
pme_order= 6
ewald_rtol   = 1e-06
ewald_geometry   = 3d
optimize_fft = yes
tcoupl  = Nose-Hoover
tc-grps = System
tau_t   = 0.4
ref_t   = 300
; Pressure coupling is on
pcoupl  = parrinello-rahman
pcoupltype  = isotropic
tau_p   = 2.0
ref_p   = 1.0
compressibility = 4.5e-5
refcoord-scaling = com
DispCorr= EnerPres
comm-mode   = linear



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Re: [gmx-users] Virtual Sites in protein-ligand systems

[Alan]

No, ACPYPE won’t give VS. But if I learn more about, I can try to
implement. No guarantee though.

On 30 October 2015 at 10:11, Joan Clark Nicolas 
wrote:

> I am trying to run MD calculations using a 5 fs timestep, so I need tu use
> Virtual Sites. The problem is that I generate ligand topology with acpype
> and then I add it to the protein topology, so the VS of the ligand are not
> generated. Maybe there is a way to generate VS for the ligand with acpype?
>
> And, about the [ virtual_sites* ] directive, can you tell me where can I
> read about this? maybe this is the thing I am looking for.
>
> Thank You!
>
>
>
> *Joan Clark i Nicolas*
>
> 2015-10-29 18:18 GMT+00:00 Justin Lemkul :
>
> >
> >
> > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
> >
> >> Dear gmx users,
> >> I am trying to run MD calculations on a protein-ligand system using
> >> Virtual
> >> Sites, but as I generate my protein and ligand topologies separately
> (with
> >> pdb2gmx and acpype, respectively), the VS for the ligand are not
> >> generated.
> >>
> >> Does anyone know a way to generate the VS for the ligand without adding
> it
> >> to the force field?
> >>
> >>
> > One can define any [ virtual_sites* ] directive manually in the topology.
> > pdb2gmx can build some types of virtual sites, but you'd have to tell us
> > specifically what it is you're trying to do if you want anything really
> > useful.  Soon I will upload a patch that will make virtual site
> > construction easier, and intrinsic to pdb2gmx.  I just need to find the
> > time to work out the kinks...
> >
> > -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://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [gmx-users] Virtual Sites in protein-ligand systems

[Justin Lemkul]

On 10/30/15 6:11 AM, Joan Clark Nicolas wrote:

I am trying to run MD calculations using a 5 fs timestep, so I need tu use
Virtual Sites. The problem is that I generate ligand topology with acpype
and then I add it to the protein topology, so the VS of the ligand are not
generated. Maybe there is a way to generate VS for the ligand with acpype?



At present, the simplest way forward is to take the information you have in your 
ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to 
process the whole thing and build the virtual sites on the ligand.



And, about the [ virtual_sites* ] directive, can you tell me where can I
read about this? maybe this is the thing I am looking for.



You can do this, but in addition to specifying the virtual sites (read in the 
PDF manual, it's all there), you will need to make the appropriate conversions 
in the [atoms] section and also build the coordinates for all virtual sites 
(e.g. the things that pdb2gmx does).


-Justin


Thank You!



*Joan Clark i Nicolas*

2015-10-29 18:18 GMT+00:00 Justin Lemkul :




On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:


Dear gmx users,
I am trying to run MD calculations on a protein-ligand system using
Virtual
Sites, but as I generate my protein and ligand topologies separately (with
pdb2gmx and acpype, respectively), the VS for the ligand are not
generated.

Does anyone know a way to generate the VS for the ligand without adding it
to the force field?



One can define any [ virtual_sites* ] directive manually in the topology.
pdb2gmx can build some types of virtual sites, but you'd have to tell us
specifically what it is you're trying to do if you want anything really
useful.  Soon I will upload a patch that will make virtual site
construction easier, and intrinsic to pdb2gmx.  I just need to find the
time to work out the kinks...

-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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send a mail to gmx-users-requ...@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

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

==
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Re: [gmx-users] Virtual Sites in protein-ligand systems

[Joan Clark Nicolas]

I am trying to run MD calculations using a 5 fs timestep, so I need tu use
Virtual Sites. The problem is that I generate ligand topology with acpype
and then I add it to the protein topology, so the VS of the ligand are not
generated. Maybe there is a way to generate VS for the ligand with acpype?

And, about the [ virtual_sites* ] directive, can you tell me where can I
read about this? maybe this is the thing I am looking for.

Thank You!



*Joan Clark i Nicolas*

2015-10-29 18:18 GMT+00:00 Justin Lemkul :

>
>
> On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
>
>> Dear gmx users,
>> I am trying to run MD calculations on a protein-ligand system using
>> Virtual
>> Sites, but as I generate my protein and ligand topologies separately (with
>> pdb2gmx and acpype, respectively), the VS for the ligand are not
>> generated.
>>
>> Does anyone know a way to generate the VS for the ligand without adding it
>> to the force field?
>>
>>
> One can define any [ virtual_sites* ] directive manually in the topology.
> pdb2gmx can build some types of virtual sites, but you'd have to tell us
> specifically what it is you're trying to do if you want anything really
> useful.  Soon I will upload a patch that will make virtual site
> construction easier, and intrinsic to pdb2gmx.  I just need to find the
> time to work out the kinks...
>
> -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://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-requ...@gromacs.org.
>
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Re: [gmx-users] Virtual Sites in protein-ligand systems

[Justin Lemkul]

On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:

Dear gmx users,
I am trying to run MD calculations on a protein-ligand system using Virtual
Sites, but as I generate my protein and ligand topologies separately (with
pdb2gmx and acpype, respectively), the VS for the ligand are not generated.

Does anyone know a way to generate the VS for the ligand without adding it
to the force field?



One can define any [ virtual_sites* ] directive manually in the topology. 
pdb2gmx can build some types of virtual sites, but you'd have to tell us 
specifically what it is you're trying to do if you want anything really useful. 
 Soon I will upload a patch that will make virtual site construction easier, 
and intrinsic to pdb2gmx.  I just need to find the time to work out the kinks...


-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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[gmx-users] Virtual Sites in protein-ligand systems

[Joan Clark Nicolas]

Dear gmx users,
I am trying to run MD calculations on a protein-ligand system using Virtual
Sites, but as I generate my protein and ligand topologies separately (with
pdb2gmx and acpype, respectively), the VS for the ligand are not generated.

Does anyone know a way to generate the VS for the ligand without adding it
to the force field?

Thanks!
*Joan Clark i Nicolas*
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Re: [gmx-users] Virtual Sites + Capped Termini

[Joan Clark Nicolas]

Hi again!
I think I have solved the problem adding the following lines to the  [
constrainttypes ] section of ffbonded.itp:

; constraints for capped termini
  MCH3  C   20.166426
  MCH3  C   20.166426
  N MCH320.166426
  N MCH320.166426

where 0.166426 is the constraint parameter for rigid CH3 groups.

Then I change the names of my Virtual Sites in the capped termini from MCH1
and MCH2 to MCH3 and it runs fine, but I am not sure that I am choosing the
correct parameters, especially for the N-MCH3 bond.

What do you think?

Thanks!

*Joan Clark i Nicolas*

2015-10-22 17:41 GMT+01:00 Justin Lemkul :

>
>
> On 10/22/15 9:05 AM, Joan Clark Nicolas wrote:
>
>> Dear gmx users,
>>
>> I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
>> termini and using Virtual Sites.
>> When I try to generate the tpr file with grompp, it seems that it is
>> missing some constraint parameters for the bonds of C from ACE and N from
>> NME with their respective virtual sites. The error I am receiving is the
>> one that follows:
>>
>>
>> *ERROR 1 [file topol.top, line 8967]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 2 [file topol.top, line 8968]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 3 [file topol.top, line 9505]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 4 [file topol.top, line 9506]:*
>> *  No default Constr. No Conn. types*
>>
>> where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
>> correspond to NME N-VS bonds. Can you tell me what am I doing wrong?
>>
>>
> Probably nothing, but not all constraint types are necessarily defined,
> especially for capped termini.  You will have to calculate appropriate
> [constrainttypes] for ffbonded.itp and add them.
>
> -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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[gmx-users] Virtual Sites + Capped Termini

[Joan Clark Nicolas]

Dear gmx users,

I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
termini and using Virtual Sites.
When I try to generate the tpr file with grompp, it seems that it is
missing some constraint parameters for the bonds of C from ACE and N from
NME with their respective virtual sites. The error I am receiving is the
one that follows:


*ERROR 1 [file topol.top, line 8967]:*
*  No default Constr. No Conn. types*


*ERROR 2 [file topol.top, line 8968]:*
*  No default Constr. No Conn. types*


*ERROR 3 [file topol.top, line 9505]:*
*  No default Constr. No Conn. types*


*ERROR 4 [file topol.top, line 9506]:*
*  No default Constr. No Conn. types*

where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
correspond to NME N-VS bonds. Can you tell me what am I doing wrong?

Thank you very much!

*Joan Clark i Nicolas*
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Re: [gmx-users] Virtual Sites + Capped Termini

[Justin Lemkul]

On 10/22/15 9:05 AM, Joan Clark Nicolas wrote:

Dear gmx users,

I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
termini and using Virtual Sites.
When I try to generate the tpr file with grompp, it seems that it is
missing some constraint parameters for the bonds of C from ACE and N from
NME with their respective virtual sites. The error I am receiving is the
one that follows:


*ERROR 1 [file topol.top, line 8967]:*
*  No default Constr. No Conn. types*


*ERROR 2 [file topol.top, line 8968]:*
*  No default Constr. No Conn. types*


*ERROR 3 [file topol.top, line 9505]:*
*  No default Constr. No Conn. types*


*ERROR 4 [file topol.top, line 9506]:*
*  No default Constr. No Conn. types*

where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
correspond to NME N-VS bonds. Can you tell me what am I doing wrong?



Probably nothing, but not all constraint types are necessarily defined, 
especially for capped termini.  You will have to calculate appropriate 
[constrainttypes] for ffbonded.itp and add them.


-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] Virtual sites error

[Timofey Tyugashev]

This looks very strange that from the whole assortment of the molecules 
in the force field only a humble methyl group in thymine lacks proper 
definition causes such an error.
Even nucleotides which I added myself to the force field files don't 
produce any errors
Is there any way to remedy this without significant hassle? What things 
are exactly lacking?

--

Message: 4
Date: Thu, 8 Oct 2015 11:15:17 +
From: Erik Marklund <erik.markl...@chem.ox.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Virtual sites error
Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Unfortunately, the parameters required for certain virtual sites in nucleic 
acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ


On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:

Trying to add hydrogen virtual sites to the model (using -vsites h option in 
pdb2gmx) results in a salvo of error messages when running grommp to create 
.tpr file after the solvation:

ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
  No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
  No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two MCH3 
and one MC atoms, which should serve (the way I understand the situation) as 
replacement methyl group in thymine. There are several more pairs of same 
errors corresponding to different thymine methyl groups in the DNA strands.

Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  aiaj functc0c1
2 3 2
  110   111 2
  110   112 2
  111   112 2

[ atoms ]

   110 CM321 DT C5110 0.0025 12.01   ; qtot -2.867
   111   MCH3321 DT   MC71111  0 7.517   ; qtot -2.867
   112   MCH3321 DT   MC72111  0 7.517   ; qtot -2.867
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Re: [gmx-users] Virtual sites error

[Erik Marklund]

If memory serves me right, the atom type for the carbon in the thymine ring 
lacks default constraint lengths to the dummy masses. That combination of atom 
types are not used for aminoacids. You will need to calculate what constraint 
lengths yield the correct geometry for the CH3-group, which is quite doable. It 
is sometimes pointed out however, here and elsewhere, that no vsite parameters 
have been rigorously tested for nucleic acids, only for proteins (to my 
knowledge).

Kind regards,
Erik

> On 9 Oct 2015, at 11:55, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:
> 
> 
> This looks very strange that from the whole assortment of the molecules in 
> the force field only a humble methyl group in thymine lacks proper definition 
> causes such an error.
> Even nucleotides which I added myself to the force field files don't produce 
> any errors
> Is there any way to remedy this without significant hassle? What things are 
> exactly lacking?
>> --
>> 
>> Message: 4
>> Date: Thu, 8 Oct 2015 11:15:17 +
>> From: Erik Marklund <erik.markl...@chem.ox.ac.uk>
>> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
>> Subject: Re: [gmx-users] Virtual sites error
>> Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Unfortunately, the parameters required for certain virtual sites in nucleic 
>> acids are not define in the force field files that are shipped with Gromacs.
>> 
>> Erik Marklund, PhD
>> Postdoctoral Research Fellow
>> Fulford JRF, Somerville College
>> 
>> Department of Chemistry
>> Physical & Theoretical Chemistry Laboratory
>> University of Oxford
>> South Parks Road
>> Oxford
>> OX1 3QZ
>> 
>>> On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:
>>> 
>>> Trying to add hydrogen virtual sites to the model (using -vsites h option 
>>> in pdb2gmx) results in a salvo of error messages when running grommp to 
>>> create .tpr file after the solvation:
>>> 
>>> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
>>>  No default Constr. No Conn. types
>>> 
>>> 
>>> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
>>>  No default Constr. No Conn. types
>>> 
>>> This lines in constraints section in the .itp file refer to pairs of two 
>>> MCH3 and one MC atoms, which should serve (the way I understand the 
>>> situation) as replacement methyl group in thymine. There are several more 
>>> pairs of same errors corresponding to different thymine methyl groups in 
>>> the DNA strands.
>>> 
>>> Here is the relevant sections of the itp file for the first two errors:
>>> 
>>> [ constraints ]
>>> ;  aiaj functc0c1
>>>2 3 2
>>>  110   111 2
>>>  110   112 2
>>>  111   112 2
>>> 
>>> [ atoms ]
>>> 
>>>   110 CM321 DT C5110 0.0025 12.01   ; qtot 
>>> -2.867
>>>   111   MCH3321 DT   MC71111  0 7.517   ; qtot 
>>> -2.867
>>>   112   MCH3321 DT   MC72111  0 7.517   ; qtot 
>>> -2.867
>>> -- 
>>> Gromacs Users mailing list
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Re: [gmx-users] Virtual sites error

[Erik Marklund]

Unfortunately, the parameters required for certain virtual sites in nucleic 
acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 7 Oct 2015, at 11:33, Timofey Tyugashev  wrote:
> 
> Trying to add hydrogen virtual sites to the model (using -vsites h option in 
> pdb2gmx) results in a salvo of error messages when running grommp to create 
> .tpr file after the solvation:
> 
> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
>  No default Constr. No Conn. types
> 
> 
> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
>  No default Constr. No Conn. types
> 
> This lines in constraints section in the .itp file refer to pairs of two MCH3 
> and one MC atoms, which should serve (the way I understand the situation) as 
> replacement methyl group in thymine. There are several more pairs of same 
> errors corresponding to different thymine methyl groups in the DNA strands.
> 
> Here is the relevant sections of the itp file for the first two errors:
> 
> [ constraints ]
> ;  aiaj functc0c1
>2 3 2
>  110   111 2
>  110   112 2
>  111   112 2
> 
> [ atoms ]
> 
>   110 CM321 DT C5110 0.0025 12.01   ; qtot -2.867
>   111   MCH3321 DT   MC71111  0 7.517   ; qtot -2.867
>   112   MCH3321 DT   MC72111  0 7.517   ; qtot -2.867
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[gmx-users] Virtual sites error

[Timofey Tyugashev]

Trying to add hydrogen virtual sites to the model (using -vsites h 
option in pdb2gmx) results in a salvo of error messages when running 
grommp to create .tpr file after the solvation:


ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
  No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
  No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two 
MCH3 and one MC atoms, which should serve (the way I understand the 
situation) as replacement methyl group in thymine. There are several 
more pairs of same errors corresponding to different thymine methyl 
groups in the DNA strands.


Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  aiaj functc0c1
2 3 2
  110   111 2
  110   112 2
  111   112 2

[ atoms ]

   110 CM321 DT C5110 0.0025 12.01   ; qtot 
-2.867
   111   MCH3321 DT   MC71111  0 7.517   ; qtot 
-2.867
   112   MCH3321 DT   MC72111  0 7.517   ; qtot 
-2.867

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[gmx-users] Virtual sites and diffusion coefficients for CO2

[贺仲金]

Dear all,

I am using rigid CO2 model with virtual sites. The bond lengthe and LJ 
parameters are taken from TraPPE force field (Vapor–liquid equilibria of 
mixtures containing alkanes, carbon dioxide, and nitrogen. JJ Potoff, JI 
Siepmann. AIChE journal 47 (7), 1676-1682, 2001. 469). I followed Justin A. 
Lemkul's tutorial to construct the virtual sites 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html).
 I find everything is OK except for the diffusion coeffients for CO2 are 
strange. The value with virtual sites (144.3087 (+/- 2.4934) 1e-5 cm^2/s) is 
half of that without virtual sites (282.5691 (+/- 20.2510) 1e-5 cm^2/s) . I 
just simulated 256 CO2 molecules at 298K and 55.2 bar with GROMACS 5.0.4. The 
itp files for CO2 with virtual sites is attched below. I found someone else 
also encounter such problems as shown in 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-February/095205.html
 and http://comments.gmane.org/gmane.science.biology.gromacs.user/23002 , and 
nobody solve out the origin of this issue.  Could anybody help me to check the 
itp files I build and find out the origin of this issue. Thanks in advance!



CO2_atomtypes.itp
[ atomtypes ]
;name  bond_typemasscharge   ptype  sigma  epsilon
OZOZ  15.99940   0.A   3.0500e-01  0.656806e0
CZCZ  12.01100   0.A   2.8000e-01  0.224478e0
MCO   MCO   0.0000.000 A  0.000  0.000


CO2_rigid.itp
[ moleculetype ]
; Name   nrexcl
CO2  2


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB
 1 OZ  1CO2  O1  1   -0.350.00
 2 CZ  1CO2  C  10.700.00
 3 OZ  1CO2  O2  1   -0.35  0.00
 4MCO  1CO2  M1  1 0.000  22.0049 
 5MCO  1CO2  M2  1 0.000  22.0049


[ constraints ]
; Overall structure is O1--M1---C---M2--O2 where M indicate mass centers
; There are no bonds in this system
; Instead, we fix the distance between the mass centers such that
; the virtual sites can be reconstructed
4   5   1   0.197995


[ virtual_sites2 ]
; the M1--O1 distance is 0.1161 - (0.197995/2) = 0.0171025
; the M1--M2 distance is 0.197995
; therefore, the fraction of the distance O1M2 along the M1--M2 length is 
(0.197995+0.0171025)/0.197995 = 1.0863784
; thus placing the virtual O1 sites beyond the M1--M2 distance 
; site  ai(from)  aj  funct   a
 1   4   5  1   1.0863784  ; relative to mass center 4, extends beyond 
mass center 5 
 2   4   5  1   0.5000  ; right in the middle
 3   5   4  1   1.0863784   ; as in the case of site 1


[ exclusions ]
1 2 3
2 1 3
3 1 2




itp files without Virtual sites


CO2_atomtypes.itp
[ atomtypes ]
;name  bond_typemasscharge   ptype  sigma  epsilon
OZOZ  16.   0.A   3.0500e-01  0.656806e0
CZCZ  12.   0.A   2.8000e-01  0.224478e0


CO2_rigid.itp
[ moleculetype ]
; Name   nrexcl
CO2  2


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB
 1 OZ  1CO2  O1  1   -0.3516.00
 2 CZ  1CO2  C  10.7012.00
 3 OZ  1CO2  O2  1   -0.35  16.00


[ Constraints ]
;  aiaj funct  b0  
1 2 1  0.1161  
2 3 1  0.1161   
1 3 1  0.2322




Best wishes!


Zhongjin HE
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Re: [gmx-users] Virtual sites and diffusion coefficients.

[sujithkakkat .]

Hello Mark,

 I have tested both models in simulating a variety of properties. The
original parametrization results involved predicting the critical point of
CO2 and also density at various P and T. I did several NVT simulations to
predict density-vs-pressure data. In this case the model with virtual
interaction sites gave much better results.

 In addition to this, simulations performed were performed on pure CO2
at supercritical conditions and mean square displacement was calculated for
the CO2 molecule. When compared to the reported ab initio dynamics results
the one obtained  using virtual sites gave much better agreement.

 The density of CO2 dissolved in H2O at very dilute concentrations was
also studied using both models of CO2 and the results were in good
agreement with experimental data for the model with virtual sites. In this
case the one without virtual sites also did reasonably well.

  However, the disparity appears when considering the Measn Square
displacement of dilute CO2 solution in water. Here the model without
virtual sites is closer to the experimental data.

This has become very confusing now. The original parametrization of he
model did not involve predicting the transport properties. Also in the
published results using the EPM2 model  I don't find any mention of the
virtual interaction sites.

Regards,

Sujith.


On Tue, Feb 3, 2015 at 1:40 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 With which set of parameters are you able to reproduce the original
 parametrization results?

 Mark

 On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com
 wrote:

  Dear all,
 
   I tried simulating the CO2-water mixture with CO2 at a low
  concentration (0.003 mole fraction) at various temperatures at 1 atmos.
 
  I used the EPM2 parameters for the CO2 molecules which includes a
 flexible
  OCO angle. I did a separate simulation on the similar system with CO2
 model
  constructed using virtual sites (following Justin Lemkul's tutorial) ,
 with
  the interaction parameters same as the EPM2 model.
 
  In both cases the water model TIP4P was used.
 
  I ran 5ns simulation after equilibrium was attained for the T and P
 values.
 
When plotting the mean square displacement and fitting the graph to get
  the diffusion coefficients, what I find is that the diffusion coefficient
  obtained in the case of the CO2 model using virtual sites is much higher
  (approximately two times) of that obtained for the EPM2 model without the
  virtual sites.
 
Let me know if any one came across this before. I would like to hear
 from
  the more experienced users, what they think about this.
 
  I will provide further details on the topology and MD parameters if
  necessary.
 
  Regards,
 
  Sujith.
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Re: [gmx-users] Virtual sites and diffusion coefficients.

[Mark Abraham]

Hi,

With which set of parameters are you able to reproduce the original
parametrization results?

Mark

On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com wrote:

 Dear all,

  I tried simulating the CO2-water mixture with CO2 at a low
 concentration (0.003 mole fraction) at various temperatures at 1 atmos.

 I used the EPM2 parameters for the CO2 molecules which includes a flexible
 OCO angle. I did a separate simulation on the similar system with CO2 model
 constructed using virtual sites (following Justin Lemkul's tutorial) , with
 the interaction parameters same as the EPM2 model.

 In both cases the water model TIP4P was used.

 I ran 5ns simulation after equilibrium was attained for the T and P values.

   When plotting the mean square displacement and fitting the graph to get
 the diffusion coefficients, what I find is that the diffusion coefficient
 obtained in the case of the CO2 model using virtual sites is much higher
 (approximately two times) of that obtained for the EPM2 model without the
 virtual sites.

   Let me know if any one came across this before. I would like to hear from
 the more experienced users, what they think about this.

 I will provide further details on the topology and MD parameters if
 necessary.

 Regards,

 Sujith.
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Re: [gmx-users] Virtual sites and diffusion coefficients.

[Justin Lemkul]

On 2/3/15 3:56 AM, sujithkakkat . wrote:

Hello Mark,

  I have tested both models in simulating a variety of properties. The
original parametrization results involved predicting the critical point of
CO2 and also density at various P and T. I did several NVT simulations to
predict density-vs-pressure data. In this case the model with virtual
interaction sites gave much better results.

  In addition to this, simulations performed were performed on pure CO2
at supercritical conditions and mean square displacement was calculated for
the CO2 molecule. When compared to the reported ab initio dynamics results
the one obtained  using virtual sites gave much better agreement.

  The density of CO2 dissolved in H2O at very dilute concentrations was
also studied using both models of CO2 and the results were in good
agreement with experimental data for the model with virtual sites. In this
case the one without virtual sites also did reasonably well.

   However, the disparity appears when considering the Measn Square
displacement of dilute CO2 solution in water. Here the model without
virtual sites is closer to the experimental data.

 This has become very confusing now. The original parametrization of he
model did not involve predicting the transport properties. Also in the
published results using the EPM2 model  I don't find any mention of the
virtual interaction sites.



I'm rather amazed that my tutorial model works so well, but please note the 
strong caution I wrote in the topology.  There is no validation of this model at 
all, anywhere in the literature.  Any reviewer of your work is going to 
certainly want an explanation of the parameters, and some model from a tutorial 
that says it isn't guaranteed to be physically valid probably isn't going to 
satisfy them.


-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] Virtual Sites

[Roland Schulz]

Hi,

I haven't tried it but it should work if you set verlet-buffer-drift=-1 and
set rlist manually.

Roland


On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten bv0...@brocku.ca wrote:

 I am trying to add virtual sites to a simulation with no mass or charge,
 just
 to make tracking the center of mass of groups later easier later on.

 However, I keep getting the warning The mass of a vsiten constructing atom
 is = 0 when i run grompp.

 Here's the section of my .itp file where i have defined them:

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
 chargeB  massB
 ; residue   1 CHX rtp CHX  q  0.0
  1   CLAL  1CHXCL1  1 -0.151 35.453   ;
 qtot
 -0.151
 .
 .
 .
 .

 63 CA  1CHXCZ2 63  0.083 12.011   ;
 qtot
 0.144
 64   CLAL  1CHXCL2 64 -0.144 35.453   ;
 qtot
 0
 65   MCH3  1CHX V1 65  0  0   ;
 66   MCH3  1CHX V2 66  0  0   ;
 67   MCH3  1CHX V3 67  0  0   ;
 68   MCH3  1CHX V4 68  0  0   ;
 69   MCH3  1CHX V5 69  0  0   ;
 70   MCH3  1CHX V6 70  0  0   ;
 71   MCH3  1CHX V7 71  0  0   ;
 72   MCH3  1CHX V8 72  0  0   ;
 73   MCH3  1CHX V9 73  0  0   ;
 74   MCH3  1CHXV10 74  0  0   ;
 75   MCH3  1CHXV11 75  0  0   ;
 76   MCH3  1CHXV12 76  0  0   ;

 [virtual_sitesn]
 65  2   8 9 10 11
 66  2   2 3 6 7
 67  2   1 4 5 12 13
 68  2   14 15 16 17 18
 69  2   19 20 21 22 23
 70  2   24 25 26 27 28 29 30 31 32
 71  2   33 34 35 36 37 38 39 40 41
 72  2   49 50 51 52 53
 73  2   44 45 46 47 48
 74  2   42 43 54 57 58
 75  2   55 56 59 60
 76  2   61 62 63 64


 Am I defining something wrong here?

 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Virtual Sites

[Brad Van Oosten]

I am trying to add virtual sites to a simulation with no mass or charge, just
to make tracking the center of mass of groups later easier later on.  

However, I keep getting the warning The mass of a vsiten constructing atom
is = 0 when i run grompp.

Here's the section of my .itp file where i have defined them:

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB   
chargeB  massB
; residue   1 CHX rtp CHX  q  0.0
 1   CLAL  1CHXCL1  1 -0.151 35.453   ; qtot
-0.151
.
.
.
.

63 CA  1CHXCZ2 63  0.083 12.011   ; qtot
0.144
64   CLAL  1CHXCL2 64 -0.144 35.453   ; qtot
0
65   MCH3  1CHX V1 65  0  0   ; 
66   MCH3  1CHX V2 66  0  0   ; 
67   MCH3  1CHX V3 67  0  0   ; 
68   MCH3  1CHX V4 68  0  0   ; 
69   MCH3  1CHX V5 69  0  0   ; 
70   MCH3  1CHX V6 70  0  0   ; 
71   MCH3  1CHX V7 71  0  0   ; 
72   MCH3  1CHX V8 72  0  0   ; 
73   MCH3  1CHX V9 73  0  0   ; 
74   MCH3  1CHXV10 74  0  0   ; 
75   MCH3  1CHXV11 75  0  0   ;
76   MCH3  1CHXV12 76  0  0   ;

[virtual_sitesn]
65  2   8 9 10 11 
66  2   2 3 6 7 
67  2   1 4 5 12 13
68  2   14 15 16 17 18
69  2   19 20 21 22 23
70  2   24 25 26 27 28 29 30 31 32
71  2   33 34 35 36 37 38 39 40 41
72  2   49 50 51 52 53
73  2   44 45 46 47 48
74  2   42 43 54 57 58
75  2   55 56 59 60
76  2   61 62 63 64


Am I defining something wrong here?

--
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http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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