subject:"\[gmx\-users\] minimum distance between the protein and its mirror image"

Re: [gmx-users] minimum distance between the protein and its mirror image

2016-08-30 Thread Justin Lemkul




On 8/29/16 9:20 PM, OuyangYanhua wrote:

The minimum protein-image distance is less than the value 2.0nm, such as t 
around 1.6nm above. Does it mean my simulation is failed in the box size set?


Please read the first sentence of my previous reply.

-Justin


在 2016年8月29日，下午8:58，Justin Lemkul  写道：



On 8/29/16 5:02 AM, YanhuaOuyang wrote:

Hi,
  I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
  Then I use "gmx mindist " to  check  if a protein has seen its periodic image during 
simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg 
-pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
   02.800  5.225  7.200  7.200  7.200
   22.793  5.136  7.200  7.200  7.200
   42.804  5.002  7.200  7.200  7.200
   62.777  5.176  7.200  7.200  7.200
   82.820  5.187  7.200  7.200  7.200
   10   2.871  5.043  7.200  7.200  7.200
   12   2.788  5.089  7.200  7.200  7.200
   14   2.882  4.892  7.200  7.200  7.200
  
   5154 4.153  3.415  7.200  7.200  7.200
   5156 4.222  3.483  7.200  7.200  7.200
   5158 4.154  3.608  7.200  7.200  7.200
   5172 3.607  4.124  7.200  7.200  7.200
   5174 3.556  4.140  7.200  7.200  7.200
   5176 3.303  4.430  7.200  7.200  7.200
   5178 3.291  4.297  7.200  7.200  7.200
   ...
   5880 1.659  5.595  7.200  7.200  7.200
   5882 1.787  5.564  7.200  7.200  7.200
   5884 1.718  5.575  7.200  7.200  7.200
   5886 1.669  5.654  7.200  7.200  7.200
   5888 1.636  5.752  7.200  7.200  7.200
   5890 1.590  5.761  7.200  7.200  7.200
   5892 1.620  5.786  7.200  7.200  7.200
   5894 1.513  5.791  7.200  7.200  7.200
   5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?


It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin 
shell of water around the protein, though, which means there could be some 
artificial ordering, but whether or not that's enough to seriously perturb the 
dynamics is not immediately clear.


which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?



Protein.  You need to verify that all protein atoms behaved correctly.  CA 
atoms are unlikely to ever see their own periodic images unless you have done 
something horribly wrong in setting up your box.

-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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--
==

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] minimum distance between the protein and its mirror image

2016-08-29 Thread OuyangYanhua

The minimum protein-image distance is less than the value 2.0nm, such as t 
around 1.6nm above. Does it mean my simulation is failed in the box size set?
> 在 2016年8月29日，下午8:58，Justin Lemkul  写道：
> 
> 
> 
> On 8/29/16 5:02 AM, YanhuaOuyang wrote:
>> Hi,
>>   I am running a REMD of a disordered protein, I visualized the trajectory 
>> in VMD and I found that the protein is very close to the box edge.
>>   Then I use "gmx mindist " to  check  if a protein has seen its periodic 
>> image during simulation. When I used the command "gmx mindist -f remd_01.pdb 
>> -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose 
>> some data from  mindist.xvg, they are as follow:
>>02.800  5.225  7.200  7.200  7.200
>>22.793  5.136  7.200  7.200  7.200
>>42.804  5.002  7.200  7.200  7.200
>>62.777  5.176  7.200  7.200  7.200
>>82.820  5.187  7.200  7.200  7.200
>>10   2.871  5.043  7.200  7.200  7.200
>>12   2.788  5.089  7.200  7.200  7.200
>>14   2.882  4.892  7.200  7.200  7.200
>>   
>>5154 4.153  3.415  7.200  7.200  7.200
>>5156 4.222  3.483  7.200  7.200  7.200
>>5158 4.154  3.608  7.200  7.200  7.200
>>5172 3.607  4.124  7.200  7.200  7.200
>>5174 3.556  4.140  7.200  7.200  7.200
>>5176 3.303  4.430  7.200  7.200  7.200
>>5178 3.291  4.297  7.200  7.200  7.200
>>...
>>5880 1.659  5.595  7.200  7.200  7.200
>>5882 1.787  5.564  7.200  7.200  7.200
>>5884 1.718  5.575  7.200  7.200  7.200
>>5886 1.669  5.654  7.200  7.200  7.200
>>5888 1.636  5.752  7.200  7.200  7.200
>>5890 1.590  5.761  7.200  7.200  7.200
>>5892 1.620  5.786  7.200  7.200  7.200
>>5894 1.513  5.791  7.200  7.200  7.200
>>5896 1.523  5.908  7.200  7.200  7.200
>> I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
>> between the outside of protein and the edge of box is 1.0 nm. the Minimum 
>> distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
>> While the deal value should be at least 2.0 nm, which is double the cutoff.
>> Do anyone knows the simulation is normal and if a protein has seen its 
>> periodic image during simulation?
> 
> It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very 
> thin shell of water around the protein, though, which means there could be 
> some artificial ordering, but whether or not that's enough to seriously 
> perturb the dynamics is not immediately clear.
> 
>> which group should I choose when i using gmx mindist, protein, C-alpha or 
>> some else?
>> 
> 
> Protein.  You need to verify that all protein atoms behaved correctly.  CA 
> atoms are unlikely to ever see their own periodic images unless you have done 
> something horribly wrong in setting up your box.
> 
> -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] minimum distance between the protein and its mirror image

2016-08-29 Thread Justin Lemkul




On 8/29/16 5:02 AM, YanhuaOuyang wrote:

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic image during 
simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg 
-pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
02.800  5.225  7.200  7.200  7.200
22.793  5.136  7.200  7.200  7.200
42.804  5.002  7.200  7.200  7.200
62.777  5.176  7.200  7.200  7.200
82.820  5.187  7.200  7.200  7.200
10   2.871  5.043  7.200  7.200  7.200
12   2.788  5.089  7.200  7.200  7.200
14   2.882  4.892  7.200  7.200  7.200
   
5154 4.153  3.415  7.200  7.200  7.200
5156 4.222  3.483  7.200  7.200  7.200
5158 4.154  3.608  7.200  7.200  7.200
5172 3.607  4.124  7.200  7.200  7.200
5174 3.556  4.140  7.200  7.200  7.200
5176 3.303  4.430  7.200  7.200  7.200
5178 3.291  4.297  7.200  7.200  7.200
...
5880 1.659  5.595  7.200  7.200  7.200
5882 1.787  5.564  7.200  7.200  7.200
5884 1.718  5.575  7.200  7.200  7.200
5886 1.669  5.654  7.200  7.200  7.200
5888 1.636  5.752  7.200  7.200  7.200
5890 1.590  5.761  7.200  7.200  7.200
5892 1.620  5.786  7.200  7.200  7.200
5894 1.513  5.791  7.200  7.200  7.200
5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?


It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin 
shell of water around the protein, though, which means there could be some 
artificial ordering, but whether or not that's enough to seriously perturb the 
dynamics is not immediately clear.



which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?



Protein.  You need to verify that all protein atoms behaved correctly.  CA atoms 
are unlikely to ever see their own periodic images unless you have done 
something horribly wrong in setting up your box.


-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

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

[gmx-users] minimum distance between the protein and its mirror image

2016-08-29 Thread YanhuaOuyang

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic 
image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s 
remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some 
data from  mindist.xvg, they are as follow:
02.800  5.225  7.200  7.200  7.200
22.793  5.136  7.200  7.200  7.200
42.804  5.002  7.200  7.200  7.200
62.777  5.176  7.200  7.200  7.200
82.820  5.187  7.200  7.200  7.200
10   2.871  5.043  7.200  7.200  7.200
12   2.788  5.089  7.200  7.200  7.200
14   2.882  4.892  7.200  7.200  7.200
   
5154 4.153  3.415  7.200  7.200  7.200
5156 4.222  3.483  7.200  7.200  7.200
5158 4.154  3.608  7.200  7.200  7.200
5172 3.607  4.124  7.200  7.200  7.200
5174 3.556  4.140  7.200  7.200  7.200
5176 3.303  4.430  7.200  7.200  7.200
5178 3.291  4.297  7.200  7.200  7.200
...
5880 1.659  5.595  7.200  7.200  7.200
5882 1.787  5.564  7.200  7.200  7.200
5884 1.718  5.575  7.200  7.200  7.200
5886 1.669  5.654  7.200  7.200  7.200
5888 1.636  5.752  7.200  7.200  7.200
5890 1.590  5.761  7.200  7.200  7.200
5892 1.620  5.786  7.200  7.200  7.200
5894 1.513  5.791  7.200  7.200  7.200
5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?
which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] minimum distance between the protein and its mirror image

Re: [gmx-users] minimum distance between the protein and its mirror image

Re: [gmx-users] minimum distance between the protein and its mirror image

[gmx-users] minimum distance between the protein and its mirror image

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