Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

I see. Now I understand what "pull-start" option means. Changing that
option made it work! Thank you Justin.

On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul  wrote:

>
>
> On 8/7/16 1:21 PM, Dan Gil wrote:
>
>> In Gromacs/4.6, I used init to define the distance from the solvent COM
>> that the solute should be pulled to. Has it changed for Gromacs/5.1?
>>
>>
> Nothing has changed except (1) syntax and (2) the ability to now apply
> multiple restraints simultaneously.  Everything with respect to setting
> references distances, etc. is functionally the same.
>
> What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
>> the solvent COM?
>>
>>
> You can do that with "pull-coord1-init = X" and "pull-start = no" but this
> is setting the reference distance to X, so if the initial coordinates are
> far from that value, you're imparting a large force to start, which may not
> be stable. It may work, but those initial steps are going to be dicey.
>
> -Justin
>
>
> Here is the section I think you are talking about also:
>> Pull group 1 'a_Cooh' has 1 atoms
>> Pull group 2 'SOL' has 5715 atoms
>> Number of degrees of freedom in T-Coupling group System is 44530.00
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>>1 1 0
>>2  5715 18540   3.011 nm  3.011 nm
>>
>> On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/7/16 1:13 PM, Dan Gil wrote:
>>>
>>> Hi,

 I've made the change you suggested. The output file pullx.xvg has
 changed
 from something like:

 @ s0 legend "1"
 @ s1 legend "1 dZ"
 0. 3.01072 3.01072
 0.2000 2.98101 2.98101
 0.4000 2.94186 2.94186
 0.6000 2.95316 2.95316

 to this:

 @ s0 legend "1"
 @ s1 legend "1 dZ"
 0. 3.01072 -3.01072
 0.2000 2.98101 -2.98101
 0.4000 2.94186 -2.94186
 0.6000 2.95316 -2.95316

 The second column should the COM of the solvent, the third column should
 be
 the position of a_Cooh. I am still wondering what is going on, since
 init
 =
 0.



 pull-coord1-start= yes
>>>
>>> grompp tells you what the reference distance is at the start; check to
>>> make sure this is what you want it to be.  pull-coord1-init = 0 means
>>> "don't add anything extra to what is already there."
>>>
>>>
>>> -Justin
>>>
>>>
>>> On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:



> On 8/7/16 11:35 AM, Dan Gil wrote:
>
> Hi,
>
>>
>> The pullx.xvg file is returning the coordinates of the solvent, and
>> not
>> the
>> solute (a_Cooh) as I want.
>> The solute is being pulled in a coordinate other than Z, although I
>> specify:
>>  pull-coord1-dim =N N Y
>> What is going on here?
>>
>>
>> Swap
>>
> pull-coord1-groups = 1 2
> for
> pull-coord1-groups = 2 1
>
> to do what you had been doing in the previous version.  You've inverted
> the pull vector relative to the 4.6 settings.
>
> -Justin
>
>
> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>
> billy.williams-noo...@monash.edu> wrote:
>>
>> Hi All,
>>
>>
>>> I'm having a similar problem and wouldn't mind some advice either.  I
>>> am
>>> getting LINCS warnings on one cluster that I run my sampling on, but
>>> the
>>> pull-code works fine on other clusters we have access to, which is
>>> making
>>> me doubt the entire process.
>>>
>>> Best regards,
>>>
>>> Billy
>>>
>>> On 7 August 2016 at 03:34, Dan Gil  wrote:
>>>
>>> Hi,
>>>
>>>
 I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
 .mdp
 file that I am confused with.

 I am pulling an atom of solute, indexed a_Cooh, towards the COM of

 solvent.

>>>
>>> This is a slab geometry, with the plane normal to the z-axis
>>> direction.
>>>

 My

>>>
>>> output (pullx.xvg) should contain the deltaZ value between the
>>> solute Z
>>>
 coordinate and solvent COM z coordinate. With my current Gromacs/5.1
 attempt, I don't think I am getting the correct results.

 On Gromacs/4.6:
 pull =umbrella
 pull_geometry =distance
 pull_dim =N N Y
 pull_init1 =0
 pull_k1 =100
 pull_nstxout =100
 pull_group0 =SOL
 pull_group1 =a_Cooh

 My attempt with Gromacs/5.1:
 pull =yes
 pull-ngroups= 2
 pull-ncoords= 1
 pull-group1-name = a_Cooh
 pull-group2-name = SOL
 pull-coord1-type  = umbrella
 pull-coord1-geometry =distance
 pull-coord1-groups = 1 2
 

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Justin Lemkul]

On 8/7/16 1:21 PM, Dan Gil wrote:

In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?



Nothing has changed except (1) syntax and (2) the ability to now apply multiple 
restraints simultaneously.  Everything with respect to setting references 
distances, etc. is functionally the same.



What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?



You can do that with "pull-coord1-init = X" and "pull-start = no" but this is 
setting the reference distance to X, so if the initial coordinates are far from 
that value, you're imparting a large force to start, which may not be stable. 
It may work, but those initial steps are going to be dicey.


-Justin


Here is the section I think you are talking about also:
Pull group 1 'a_Cooh' has 1 atoms
Pull group 2 'SOL' has 5715 atoms
Number of degrees of freedom in T-Coupling group System is 44530.00
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1 1 0
   2  5715 18540   3.011 nm  3.011 nm

On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul  wrote:




On 8/7/16 1:13 PM, Dan Gil wrote:


Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should
be
the position of a_Cooh. I am still wondering what is going on, since init
=
0.




pull-coord1-start= yes

grompp tells you what the reference distance is at the start; check to
make sure this is what you want it to be.  pull-coord1-init = 0 means
"don't add anything extra to what is already there."


-Justin



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:




On 8/7/16 11:35 AM, Dan Gil wrote:

Hi,


The pullx.xvg file is returning the coordinates of the solvent, and not
the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I
specify:
 pull-coord1-dim =N N Y
What is going on here?


Swap

pull-coord1-groups = 1 2
for
pull-coord1-groups = 2 1

to do what you had been doing in the previous version.  You've inverted
the pull vector relative to the 4.6 settings.

-Justin


On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <


billy.williams-noo...@monash.edu> wrote:

Hi All,



I'm having a similar problem and wouldn't mind some advice either.  I
am
getting LINCS warnings on one cluster that I run my sampling on, but
the
pull-code works fine on other clusters we have access to, which is
making
me doubt the entire process.

Best regards,

Billy

On 7 August 2016 at 03:34, Dan Gil  wrote:

Hi,



I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
.mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of

solvent.


This is a slab geometry, with the plane normal to the z-axis direction.


My


output (pullx.xvg) should contain the deltaZ value between the solute Z

coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?

What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?

Here is the section I think you are talking about also:
Pull group 1 'a_Cooh' has 1 atoms
Pull group 2 'SOL' has 5715 atoms
Number of degrees of freedom in T-Coupling group System is 44530.00
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1 1 0
   2  5715 18540   3.011 nm  3.011 nm

On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul  wrote:

>
>
> On 8/7/16 1:13 PM, Dan Gil wrote:
>
>> Hi,
>>
>> I've made the change you suggested. The output file pullx.xvg has changed
>> from something like:
>>
>> @ s0 legend "1"
>> @ s1 legend "1 dZ"
>> 0. 3.01072 3.01072
>> 0.2000 2.98101 2.98101
>> 0.4000 2.94186 2.94186
>> 0.6000 2.95316 2.95316
>>
>> to this:
>>
>> @ s0 legend "1"
>> @ s1 legend "1 dZ"
>> 0. 3.01072 -3.01072
>> 0.2000 2.98101 -2.98101
>> 0.4000 2.94186 -2.94186
>> 0.6000 2.95316 -2.95316
>>
>> The second column should the COM of the solvent, the third column should
>> be
>> the position of a_Cooh. I am still wondering what is going on, since init
>> =
>> 0.
>>
>>
>>
> pull-coord1-start= yes
>
> grompp tells you what the reference distance is at the start; check to
> make sure this is what you want it to be.  pull-coord1-init = 0 means
> "don't add anything extra to what is already there."
>
>
> -Justin
>
>
>> On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/7/16 11:35 AM, Dan Gil wrote:
>>>
>>> Hi,

 The pullx.xvg file is returning the coordinates of the solvent, and not
 the
 solute (a_Cooh) as I want.
 The solute is being pulled in a coordinate other than Z, although I
 specify:
  pull-coord1-dim =N N Y
 What is going on here?


 Swap
>>> pull-coord1-groups = 1 2
>>> for
>>> pull-coord1-groups = 2 1
>>>
>>> to do what you had been doing in the previous version.  You've inverted
>>> the pull vector relative to the 4.6 settings.
>>>
>>> -Justin
>>>
>>>
>>> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>>>
 billy.williams-noo...@monash.edu> wrote:

 Hi All,

>
> I'm having a similar problem and wouldn't mind some advice either.  I
> am
> getting LINCS warnings on one cluster that I run my sampling on, but
> the
> pull-code works fine on other clusters we have access to, which is
> making
> me doubt the entire process.
>
> Best regards,
>
> Billy
>
> On 7 August 2016 at 03:34, Dan Gil  wrote:
>
> Hi,
>
>>
>> I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
>> .mdp
>> file that I am confused with.
>>
>> I am pulling an atom of solute, indexed a_Cooh, towards the COM of
>>
>> solvent.
>
> This is a slab geometry, with the plane normal to the z-axis direction.
>>
>> My
>
> output (pullx.xvg) should contain the deltaZ value between the solute Z
>> coordinate and solvent COM z coordinate. With my current Gromacs/5.1
>> attempt, I don't think I am getting the correct results.
>>
>> On Gromacs/4.6:
>> pull =umbrella
>> pull_geometry =distance
>> pull_dim =N N Y
>> pull_init1 =0
>> pull_k1 =100
>> pull_nstxout =100
>> pull_group0 =SOL
>> pull_group1 =a_Cooh
>>
>> My attempt with Gromacs/5.1:
>> pull =yes
>> pull-ngroups= 2
>> pull-ncoords= 1
>> pull-group1-name = a_Cooh
>> pull-group2-name = SOL
>> pull-coord1-type  = umbrella
>> pull-coord1-geometry =distance
>> pull-coord1-groups = 1 2
>> pull-coord1-dim =N N Y
>> pull-coord1-start= yes
>> pull-coord1-init  =0
>> pull-coord1-k=1000
>> pull-print-components = yes
>> pull_nstxout =100
>>
>> Best Regards,
>>
>> Dan
>> --
>> 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
>>
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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.
>>
>>
>>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
>  trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> --
> Gromacs Users mailing list
>
> * Please search the archive at 

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Justin Lemkul]

On 8/7/16 1:13 PM, Dan Gil wrote:

Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should be
the position of a_Cooh. I am still wondering what is going on, since init =
0.




pull-coord1-start= yes

grompp tells you what the reference distance is at the start; check to make sure 
this is what you want it to be.  pull-coord1-init = 0 means "don't add anything 
extra to what is already there."


-Justin



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:




On 8/7/16 11:35 AM, Dan Gil wrote:


Hi,

The pullx.xvg file is returning the coordinates of the solvent, and not
the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I
specify:
 pull-coord1-dim =N N Y
What is going on here?



Swap
pull-coord1-groups = 1 2
for
pull-coord1-groups = 2 1

to do what you had been doing in the previous version.  You've inverted
the pull vector relative to the 4.6 settings.

-Justin


On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <

billy.williams-noo...@monash.edu> wrote:

Hi All,


I'm having a similar problem and wouldn't mind some advice either.  I am
getting LINCS warnings on one cluster that I run my sampling on, but the
pull-code works fine on other clusters we have access to, which is making
me doubt the entire process.

Best regards,

Billy

On 7 August 2016 at 03:34, Dan Gil  wrote:

Hi,


I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
.mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of


solvent.


This is a slab geometry, with the plane normal to the z-axis direction.


My


output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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--
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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--
==

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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--
==

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

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should be
the position of a_Cooh. I am still wondering what is going on, since init =
0.



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:

>
>
> On 8/7/16 11:35 AM, Dan Gil wrote:
>
>> Hi,
>>
>> The pullx.xvg file is returning the coordinates of the solvent, and not
>> the
>> solute (a_Cooh) as I want.
>> The solute is being pulled in a coordinate other than Z, although I
>> specify:
>>  pull-coord1-dim =N N Y
>> What is going on here?
>>
>>
> Swap
> pull-coord1-groups = 1 2
> for
> pull-coord1-groups = 2 1
>
> to do what you had been doing in the previous version.  You've inverted
> the pull vector relative to the 4.6 settings.
>
> -Justin
>
>
> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Hi All,
>>>
>>> I'm having a similar problem and wouldn't mind some advice either.  I am
>>> getting LINCS warnings on one cluster that I run my sampling on, but the
>>> pull-code works fine on other clusters we have access to, which is making
>>> me doubt the entire process.
>>>
>>> Best regards,
>>>
>>> Billy
>>>
>>> On 7 August 2016 at 03:34, Dan Gil  wrote:
>>>
>>> Hi,

 I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
 .mdp
 file that I am confused with.

 I am pulling an atom of solute, indexed a_Cooh, towards the COM of

>>> solvent.
>>>
 This is a slab geometry, with the plane normal to the z-axis direction.

>>> My
>>>
 output (pullx.xvg) should contain the deltaZ value between the solute Z
 coordinate and solvent COM z coordinate. With my current Gromacs/5.1
 attempt, I don't think I am getting the correct results.

 On Gromacs/4.6:
 pull =umbrella
 pull_geometry =distance
 pull_dim =N N Y
 pull_init1 =0
 pull_k1 =100
 pull_nstxout =100
 pull_group0 =SOL
 pull_group1 =a_Cooh

 My attempt with Gromacs/5.1:
 pull =yes
 pull-ngroups= 2
 pull-ncoords= 1
 pull-group1-name = a_Cooh
 pull-group2-name = SOL
 pull-coord1-type  = umbrella
 pull-coord1-geometry =distance
 pull-coord1-groups = 1 2
 pull-coord1-dim =N N Y
 pull-coord1-start= yes
 pull-coord1-init  =0
 pull-coord1-k=1000
 pull-print-components = yes
 pull_nstxout =100

 Best Regards,

 Dan
 --
 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

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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.


>>>
>>>
>>> --
>>> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>>>
>>> *LinkedIn Profile
>>> >> trk=prof-0-sb-preview-primary-button>
>>> **|*   +61420 382 557
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>> Royal Parade, Parkville, 3052
>>> --
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> --
> ==
>
> 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] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Justin Lemkul]

On 8/7/16 11:35 AM, Dan Gil wrote:

Hi,

The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
 pull-coord1-dim =N N Y
What is going on here?



Swap
pull-coord1-groups = 1 2
for
pull-coord1-groups = 2 1

to do what you had been doing in the previous version.  You've inverted the pull 
vector relative to the 4.6 settings.


-Justin


On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Hi All,

I'm having a similar problem and wouldn't mind some advice either.  I am
getting LINCS warnings on one cluster that I run my sampling on, but the
pull-code works fine on other clusters we have access to, which is making
me doubt the entire process.

Best regards,

Billy

On 7 August 2016 at 03:34, Dan Gil  wrote:


Hi,

I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of

solvent.

This is a slab geometry, with the plane normal to the z-axis direction.

My

output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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--
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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--
==

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] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
 pull-coord1-dim =N N Y
What is going on here?

On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Hi All,
>
> I'm having a similar problem and wouldn't mind some advice either.  I am
> getting LINCS warnings on one cluster that I run my sampling on, but the
> pull-code works fine on other clusters we have access to, which is making
> me doubt the entire process.
>
> Best regards,
>
> Billy
>
> On 7 August 2016 at 03:34, Dan Gil  wrote:
>
> > Hi,
> >
> > I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
> > file that I am confused with.
> >
> > I am pulling an atom of solute, indexed a_Cooh, towards the COM of
> solvent.
> > This is a slab geometry, with the plane normal to the z-axis direction.
> My
> > output (pullx.xvg) should contain the deltaZ value between the solute Z
> > coordinate and solvent COM z coordinate. With my current Gromacs/5.1
> > attempt, I don't think I am getting the correct results.
> >
> > On Gromacs/4.6:
> > pull =umbrella
> > pull_geometry =distance
> > pull_dim =N N Y
> > pull_init1 =0
> > pull_k1 =100
> > pull_nstxout =100
> > pull_group0 =SOL
> > pull_group1 =a_Cooh
> >
> > My attempt with Gromacs/5.1:
> > pull =yes
> > pull-ngroups= 2
> > pull-ncoords= 1
> > pull-group1-name = a_Cooh
> > pull-group2-name = SOL
> > pull-coord1-type  = umbrella
> > pull-coord1-geometry =distance
> > pull-coord1-groups = 1 2
> > pull-coord1-dim =N N Y
> > pull-coord1-start= yes
> > pull-coord1-init  =0
> > pull-coord1-k=1000
> > pull-print-components = yes
> > pull_nstxout =100
> >
> > Best Regards,
> >
> > Dan
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
>  trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
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Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Billy Williams-Noonan]

Hi All,

I'm having a similar problem and wouldn't mind some advice either.  I am
getting LINCS warnings on one cluster that I run my sampling on, but the
pull-code works fine on other clusters we have access to, which is making
me doubt the entire process.

Best regards,

Billy

On 7 August 2016 at 03:34, Dan Gil  wrote:

> Hi,
>
> I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
> file that I am confused with.
>
> I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent.
> This is a slab geometry, with the plane normal to the z-axis direction. My
> output (pullx.xvg) should contain the deltaZ value between the solute Z
> coordinate and solvent COM z coordinate. With my current Gromacs/5.1
> attempt, I don't think I am getting the correct results.
>
> On Gromacs/4.6:
> pull =umbrella
> pull_geometry =distance
> pull_dim =N N Y
> pull_init1 =0
> pull_k1 =100
> pull_nstxout =100
> pull_group0 =SOL
> pull_group1 =a_Cooh
>
> My attempt with Gromacs/5.1:
> pull =yes
> pull-ngroups= 2
> pull-ncoords= 1
> pull-group1-name = a_Cooh
> pull-group2-name = SOL
> pull-coord1-type  = umbrella
> pull-coord1-geometry =distance
> pull-coord1-groups = 1 2
> pull-coord1-dim =N N Y
> pull-coord1-start= yes
> pull-coord1-init  =0
> pull-coord1-k=1000
> pull-print-components = yes
> pull_nstxout =100
>
> Best Regards,
>
> Dan
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

Hi,

I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent.
This is a slab geometry, with the plane normal to the z-axis direction. My
output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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