[gmx-users] Re: ok, thank you
Williams Ernesto Miranda Delgado
wmiranda at fbio.uh.cu
Tue Nov 12 15:28:24 CET 2013
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> Today's Topics:
>
> 1. Restarting a simulation after replacing an empty md.trr file
> (arun kumar)
> 2. Re: Re: Reaction field zero and ions (Justin Lemkul)
> 3. Re: Calculating diffusion coefficient in three dimension
> (Dr. Vitaly Chaban)
> 4. Re: Re: Reaction field zero and ions (Dr. Vitaly Chaban)
> 5. Re: Re: g_analyze (Justin Lemkul)
> 6. Re: Re: g_analyze (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 12 Nov 2013 11:45:05 +0530
> From: arun kumar <arunjones.kumar89 at gmail.com>
> Subject: [gmx-users] Restarting a simulation after replacing an empty
> md.trr file
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGM9vJ8DN+FQB-cigJDvV+i1MQ7MC2CxVkdE3gsP5+LWHDSU2g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gromacs users,
>
> I am running a 50ns simulation of a protein having nearly 700 residues on
> 60 threads (Gromacs 4.6.3).
> At one point i got a disk space problem, so i have deleted the md.trr file
> and created an empty md.trr file. when i tried to restart the simulation
> from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt
> -nt
> 100 ]
> i am getting a note and an error as fallows
>
> Reading checkpoint file md.cpt generated:
> #PME-nodes mismatch,
> current program: 100
> checkpoint file: 60
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
> ...
>
> Source code file: checkpoint.c, line: 1767
> Fatal error:
> Can't read 1048576 bytes of 'md.trr' to compute checksum. The file
> has been replaced or its contents has been modified.
>
> please help me in overcoming this problem.
>
> Thanking you.
>
> --
> Arun Kumar Somavarapu
> Project-JRF
> Dr. Pawan Gupta's lab
> Protein Science and Engineering Dept,
> Institute of Microbial Tecnology,
> Sec 39-A, Chandigarh - 160036.
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Nov 2013 13:06:32 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Reaction field zero and ions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <52811CA8.5030900 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
>> Hello
>> If I did the MD simulation using PME and neutralized with ions, and I
>> want
>> to rerun this time with reaction field zero, is there any problem if I
>> keep the ions? This is for LIE calculation. I am using AMBER99SB.
>
> Why do you think it necessary to delete them?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 12 Nov 2013 13:02:54 +0100
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> Subject: Re: [gmx-users] Calculating diffusion coefficient in three
> dimension
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAPXdD+aBAY6mj_dKN6_k+mKbUTy4eYzsPDVDXJ+M-M-2zaeqnw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> MSD is 3D by default.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:
>> Dear all,
>> I am simulating a spherical lipid vesicle. I want to calculate the
>> diffusion coefficient for each lipid component in 3D. How to calculate
>> it
>> using g_msd (or any other tool like g_velacc)?
>>
>> Thank you for your concern
>>
>> --
>> With Best Wishes
>> Venkat Reddy Chirasani
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 12 Nov 2013 13:04:10 +0100
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> Subject: Re: [gmx-users] Re: Reaction field zero and ions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAPXdD+ZuWGcFdX+hymRGi7tm4PA5fNCZemR+TDswD5yqVaqPAw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> There are no problems to have ions while using Reaction-Field treatment.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
>>>
>>> Hello
>>> If I did the MD simulation using PME and neutralized with ions, and I
>>> want
>>> to rerun this time with reaction field zero, is there any problem if I
>>> keep the ions? This is for LIE calculation. I am using AMBER99SB.
>>
>>
>> Why do you think it necessary to delete them?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 12 Nov 2013 08:14:35 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: g_analyze
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <528229BB.6080504 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 11/11/13 5:39 PM, bharat gupta wrote:
>> Sorry, I attached the wrong file . Here's the average file generate from
>> one of the files I sent in my last mail. I used the command g_analyze -f
>> hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file
>> obtained
>> from this command :-
>>
>> https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg
>>
>> Now, if you see, the graph (in previous mail) and average file, both
>> correlates well. I have a doubt about interpreting the result from
>> g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
>> bonds are formed during the simulation time of 5ns to 10ns. What does
>> then
>> the average file or its graph tells ??
>>
>
> It's an average over sets. It is not equivalent to the output printed to
> the
> screen, nor is it supposed to. The value printed to the screen is the
> actual
> average of the data set of interest, as is intuitive from your values. An
> average of 4 is impossible if all the data points are in the range of 6-9.
>
> -Justin
>
>>
>>
>> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 11/11/13 4:06 AM, bharat gupta wrote:
>>>
>>>> In addition to my previous question, I have another question about
>>>> g_analyze. When I used the hbond.xvg file to get the average and
>>>> plotted
>>>> the average.xvg file I found that the average value is round 4 to 5
>>>> according to the graph. But g_analyze in its final calculation gives
>>>> 7.150
>>>> as the average values... Here's the link for the graph and result of
>>>> average value calculated by g_analyze :-
>>>>
>>>> std. dev. relative deviation of
>>>> standard --------- cumulants from
>>>> those of
>>>> set average deviation sqrt(n-1) a Gaussian
>>>> distribition
>>>> cum. 3 cum.
>>>> 4
>>>> SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.062
>>>> 0.163
>>>>
>>>> SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.495 0.153
>>>>
>>>> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
>>>>
>>>> Here's the link hbond.xvg file and its averaged file
>>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>>>
>>>>
>>> Neither of these files produce output that corresponds to the PNG image
>>> above. Both files have values in 6-9 H-bond range and thus agree with
>>> the
>>> g_analyze output, which I can reproduce. I suspect you're somehow
>>> getting
>>> your files mixed up.
>>>
>>>
>>> -Justin
>>>
>>>
>>>> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta
>>>> <bharat.85.monu at gmail.com>
>>>> wrote:
>>>>
>>>> thank you informing about g_rdf...
>>>>>
>>>>> Is it possible to dump the structure with those average water
>>>>> molecules
>>>>> interacting with the residues. I generated the hbond.log file which
>>>>> gives
>>>>> the details but I need to generate a figure for this ??
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> On 11/10/13 8:38 PM, bharat gupta wrote:
>>>>>>
>>>>>> But trjorder can be used to calculate the hydration layer or shell
>>>>>>> around
>>>>>>> residues ... Right ??
>>>>>>>
>>>>>>>
>>>>>>> Yes, but I also tend to think that integrating an RDF is also a
>>>>>>> more
>>>>>> straightforward way of doing that. With trjorder, you set some
>>>>>> arbitrary
>>>>>> cutoff that may or may not be an informed decision - with an RDF it
>>>>>> is
>>>>>> clear where the hydration layers are.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>>>>>>
>>>>>>>> Thanks for your reply. I was missing the scientific notation
>>>>>>>> part.
>>>>>>>> Now
>>>>>>>>
>>>>>>>>> everything is fine.
>>>>>>>>>
>>>>>>>>> Regarding trjorder, it doesn't measure h-bonds but gives the
>>>>>>>>> water
>>>>>>>>> nearest
>>>>>>>>> to protein.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I wouldn't try to draw any sort of comparison between the
>>>>>>>>> output of
>>>>>>>>>
>>>>>>>> trjorder and g_hbond. If you want to measure H-bonds, there's
>>>>>>>> only
>>>>>>>> one
>>>>>>>> tool for that.
>>>>>>>>
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>> --
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Postdoctoral Fellow
>>>>>>>>
>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>> School of Pharmacy
>>>>>>>> Health Sciences Facility II, Room 601
>>>>>>>> University of Maryland, Baltimore
>>>>>>>> 20 Penn St.
>>>>>>>> Baltimore, MD 21201
>>>>>>>>
>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>> Support/Mailing_Lists/Search before posting!
>>>>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>>>>> www
>>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 601
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>> Support/Mailing_Lists/Search before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>
>>> ==================================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 12 Nov 2013 08:15:25 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: g_analyze
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <528229ED.9080208 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 11/11/13 6:56 PM, bharat gupta wrote:
>> Hi,
>>
>> I tried g_select to dump the structure with the interacting water
>> molecules, but I don't know know how to do that. I searched for some
>> threads in the discussion but wasn't able to find anything related to my
>> need. Can you explain how can I do that ?
>>
>
> Start with g_select -select 'help all' and see what you can determine.
> Such
> selections are rather straightforward and have been explained several
> times on
> the list. If you need help, show us what you're doing and describe why it
> isn't
> what you want. It will ultimately save a lot of time.
>
> -Justin
>
>>
>> On Tue, Nov 12, 2013 at 7:39 AM, bharat gupta
>> <bharat.85.monu at gmail.com>wrote:
>>
>>> Sorry, I attached the wrong file . Here's the average file generate
>>> from
>>> one of the files I sent in my last mail. I used the command g_analyze
>>> -f
>>> hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file
>>> obtained
>>> from this command :-
>>>
>>> https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg
>>>
>>> Now, if you see, the graph (in previous mail) and average file, both
>>> correlates well. I have a doubt about interpreting the result from
>>> g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
>>> bonds are formed during the simulation time of 5ns to 10ns. What does
>>> then
>>> the average file or its graph tells ??
>>>
>>>
>>>
>>> On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>> On 11/11/13 4:06 AM, bharat gupta wrote:
>>>>
>>>>> In addition to my previous question, I have another question about
>>>>> g_analyze. When I used the hbond.xvg file to get the average and
>>>>> plotted
>>>>> the average.xvg file I found that the average value is round 4 to 5
>>>>> according to the graph. But g_analyze in its final calculation gives
>>>>> 7.150
>>>>> as the average values... Here's the link for the graph and result of
>>>>> average value calculated by g_analyze :-
>>>>>
>>>>> std. dev. relative deviation
>>>>> of
>>>>> standard --------- cumulants from
>>>>> those
>>>>> of
>>>>> set average deviation sqrt(n-1) a Gaussian
>>>>> distribition
>>>>> cum. 3 cum.
>>>>> 4
>>>>> SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.062
>>>>> 0.163
>>>>>
>>>>> SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.495 0.153
>>>>>
>>>>> https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
>>>>>
>>>>> Here's the link hbond.xvg file and its averaged file
>>>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>>>> https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
>>>>>
>>>>>
>>>> Neither of these files produce output that corresponds to the PNG
>>>> image
>>>> above. Both files have values in 6-9 H-bond range and thus agree with
>>>> the
>>>> g_analyze output, which I can reproduce. I suspect you're somehow
>>>> getting
>>>> your files mixed up.
>>>>
>>>>
>>>> -Justin
>>>>
>>>>
>>>>> On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta
>>>>> <bharat.85.monu at gmail.com>
>>>>> wrote:
>>>>>
>>>>> thank you informing about g_rdf...
>>>>>>
>>>>>> Is it possible to dump the structure with those average water
>>>>>> molecules
>>>>>> interacting with the residues. I generated the hbond.log file which
>>>>>> gives
>>>>>> the details but I need to generate a figure for this ??
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> On 11/10/13 8:38 PM, bharat gupta wrote:
>>>>>>>
>>>>>>> But trjorder can be used to calculate the hydration layer or
>>>>>>> shell
>>>>>>>> around
>>>>>>>> residues ... Right ??
>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, but I also tend to think that integrating an RDF is also a
>>>>>>>> more
>>>>>>> straightforward way of doing that. With trjorder, you set some
>>>>>>> arbitrary
>>>>>>> cutoff that may or may not be an informed decision - with an RDF it
>>>>>>> is
>>>>>>> clear where the hydration layers are.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> On 11/10/13 8:30 PM, bharat gupta wrote:
>>>>>>>>>
>>>>>>>>> Thanks for your reply. I was missing the scientific notation
>>>>>>>>> part.
>>>>>>>>> Now
>>>>>>>>>
>>>>>>>>>> everything is fine.
>>>>>>>>>>
>>>>>>>>>> Regarding trjorder, it doesn't measure h-bonds but gives the
>>>>>>>>>> water
>>>>>>>>>> nearest
>>>>>>>>>> to protein.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I wouldn't try to draw any sort of comparison between the
>>>>>>>>>> output
>>>>>>>>>> of
>>>>>>>>>>
>>>>>>>>> trjorder and g_hbond. If you want to measure H-bonds, there's
>>>>>>>>> only
>>>>>>>>> one
>>>>>>>>> tool for that.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -Justin
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ==================================================
>>>>>>>>>
>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>> Postdoctoral Fellow
>>>>>>>>>
>>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>>> School of Pharmacy
>>>>>>>>> Health Sciences Facility II, Room 601
>>>>>>>>> University of Maryland, Baltimore
>>>>>>>>> 20 Penn St.
>>>>>>>>> Baltimore, MD 21201
>>>>>>>>>
>>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>> --
>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>>> Support/Mailing_Lists/Search before posting!
>>>>>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>>>>>> www
>>>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Postdoctoral Fellow
>>>>>>>
>>>>>>> Department of Pharmaceutical Sciences
>>>>>>> School of Pharmacy
>>>>>>> Health Sciences Facility II, Room 601
>>>>>>> University of Maryland, Baltimore
>>>>>>> 20 Penn St.
>>>>>>> Baltimore, MD 21201
>>>>>>>
>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>> Support/Mailing_Lists/Search before posting!
>>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>
>>>> ==================================================
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>>
>>>
>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 115, Issue 52
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