Re: [gmx-users] high-temperature MD

[OuyangYanhua]

Thank you so much!
> 在 2016年10月7日，上午2:27，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道：
> 
> Depends, actually. There are reasons one might want to simulate a system at 
> 380 K in NVT using the average box volume from the 300 K NPT simulation. 
> Temperature replica exchange typically employs NVT and so might other 
> temperature-based enhanced sampling approaches. Justin's right, you have to 
> think it through, but I'm just chiming in to suggest that the answer is not 
> obvious from this thread thus far. TIP3P water doesn't boil in NPT until 
> somewhere around 550 K, so NPT at 380 K is certainly possible.
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin 
> Lemkul <jalem...@vt.edu>
> Sent: 06 October 2016 09:34:49
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] high-temperature MD
> 
> On 10/6/16 8:54 AM, OuyangYanhua wrote:
>> Dear Justin,
>>> 
>> I had run a 300K-MD, now I want to run a high-temperature(380K) MD to 
>> compare with the 300K-MD.
>> The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. 
>> So I want to know the high-temperature(380K) MD should run the same as the 
>> 300k, which means the 380k is also first equilibrated at NVT, then at NPT 
>> and production MD at NPT ensemble.
>> 
> 
> Think scientifically.  If you only want to vary the temperature, does it make
> any sense to vary the simulation protocol?
> 
> -Justin
> 
>> Best regards,
>> Ouyang
>> 
>>> 在 2016年10月6日，下午7:22，Justin Lemkul <jalem...@vt.edu> 写道：
>>> 
>>> 
>>> 
>>> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>>>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As 
>>>> we
>>>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>>>> production MD at NPT ensemble normally. Does someone know whether the 
>>>> 380K-MD
>>>> can only  perform at NVT ensemble since the temperature(380K) is a high
>>>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>>>> 
>>> 
>>> 380 K is not very high.  What you choose to do needs to be based on 
>>> whatever real-world conditions you want to model.
>>> 
>>> -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] high-temperature MD

[OuyangYanhua]

Dear Justin,
> 
I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare 
with the 300K-MD.
The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So 
I want to know the high-temperature(380K) MD should run the same as the 300k, 
which means the 380k is also first equilibrated at NVT, then at NPT and 
production MD at NPT ensemble.

Best regards,
Ouyang

> 在 2016年10月6日，下午7:22，Justin Lemkul  写道：
> 
> 
> 
> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we
>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>> production MD at NPT ensemble normally. Does someone know whether the 380K-MD
>> can only  perform at NVT ensemble since the temperature(380K) is a high
>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>> 
> 
> 380 K is not very high.  What you choose to do needs to be based on whatever 
> real-world conditions you want to model.
> 
> -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] minimum distance between the protein and its mirror image

[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 
> 
> 
> ==
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[gmx-users] Failed to lock: pre.log

[OuyangYanhua]

Hi,
I am running a 100ns-REMD with 50 replicas. when continuing the REMD by 
appending to the old output files, such error happened: "Fatal error:Failed to 
lock: md1.log. Already running simulation?”
Then I had a test of 5 replicas. I limit the run time for 10 minutes 
for every short REMD and continue the REMD for at least 4 times. The test went 
sccessfully. 
why the log files are locked when I run 50 replicas REMD,how to solve 
it?  And why is OK to continue the test REMD of 5 replicas on the same system?

Best regards,
Ouyang.
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your helpful example.
> 在 2016年6月20日，下午11:17，Marlon Sidore <marlon.sid...@gmail.com> 写道：
> 
> Hi,
> 
> What you want is to convert these from amber (kcal) to gromacs (kJ). I
> followed successfully another post from the mailing list here:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html
> 
> What you should do is make sure your conversion is right, by taking an
> example from the amber forcefield in amber format and its equivalent in
> gromacs format, before applying that conversion on your new parameters.
> 
> Hope that helps.
> 
> Marlon Sidore
> 
> 
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
> 
> 
> 2016-06-20 16:22 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>:
> 
>> Hi,
>> 
>> It sounds like what you want to look for is the documentation for those
>> file formats.
>> 
>> Mark
>> 
>> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
>> 
>>> Hi,
>>> I am simulating a protein phosphorylated on Ser and Thr residues using
>>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>>> phophorylation parameters in the
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>>> difficult for me to read the parameters and statistics in the frcmod and
>>> off files. So I have trouble in converting the statistics in framod files
>>> and off file to gromacs files, such as .rtp, ffbond.itp.
>>> 
>>> Best regards,
>>> Ouyang
>>> --
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your recommend.
> 在 2016年6月20日，下午10:22，Mark Abraham <mark.j.abra...@gmail.com> 写道：
> 
> Hi,
> 
> It sounds like what you want to look for is the documentation for those
> file formats.
> 
> Mark
> 
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
> 
>> Hi,
>> I am simulating a protein phosphorylated on Ser and Thr residues using
>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>> phophorylation parameters in the
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>> difficult for me to read the parameters and statistics in the frcmod and
>> off files. So I have trouble in converting the statistics in framod files
>> and off file to gromacs files, such as .rtp, ffbond.itp.
>> 
>> Best regards,
>> Ouyang
>> --
>> Gromacs Users mailing list
>> 
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] Average exchange probability when extending REMD

[OuyangYanhua]

Sorry, I am a little confused, what you mean is that the gromacs cannot 
automatically combine the data of the both  in the replica exchange statistics 
section. Maybe myself need write some program to combine the first part data 
and the extended data to get the average probability  of whole REMD?
> 在 2016年6月15日，下午9:34，Mark Abraham <mark.j.abra...@gmail.com> 写道：
> 
> Hi,
> 
> That's never been implemented, unfortunately.
> 
> Mark
> 
> On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote:
> 
>> Hi,
>> I extended the REMD of a protein in a explicit water and append the data
>> to the old ones and it appended. However, at the end of the .log files, the
>> replica exchange statistics section only contains the data of  extended
>> time, it  did not combine  the former statistics and the extended
>> statistics. why? and how to combine the both statistics.
>> 
>> Best regards,
>> Ouyang
>> --
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[gmx-users] Average exchange probability when extending REMD

[OuyangYanhua]

Hi,
I extended the REMD of a protein in a explicit water and append the data to the 
old ones and it appended. However, at the end of the .log files, the replica 
exchange statistics section only contains the data of  extended time, it  did 
not combine  the former statistics and the extended statistics. why? and how to 
combine the both statistics.

Best regards,
Ouyang
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