<p dir="ltr">Do you know wich version of gromacs works with this gpu?the page of gromacs says that 9800gt is compatible,but unfortunaly its not true.<br>
Thank you</p>
<div class="quote">Em 25/09/2015 5:44 PM, gromacs.org_gmx-users-request@maillist.sys.kth.se escreveu:<br type='attribution'><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br />
<br />
1. Gromacs says that may GeForce 9800gt is incompatible any<br />
help? (Juliano Braz Carregal)<br />
2. Re: Gromacs says that may GeForce 9800gt is incompatible any<br />
help? (Repic Matej)<br />
3. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)<br />
4. Re: GROMACS with AMBER heme parameters (Justin Lemkul)<br />
5. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)<br />
6. Re: GROMACS with AMBER heme parameters (Justin Lemkul)<br />
<br />
<br />
----------------------------------------------------------------------<br />
<br />
Message: 1<br />
Date: Fri, 25 Sep 2015 15:46:29 -0300<br />
From: Juliano Braz Carregal <julianocarregal@hotmail.com><br />
To: gromacs.org_gmx-users@maillist.sys.kth.se<br />
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is<br />
incompatible any help?<br />
Message-ID: <SNT406-EAS4017586F92E165604307495B8420@phx.gbl><br />
Content-Type: text/plain; charset="us-ascii"<br />
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------------------------------<br />
<br />
Message: 2<br />
Date: Fri, 25 Sep 2015 19:15:43 +0000<br />
From: Repic Matej <matej.repic@epfl.ch><br />
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br />
Subject: Re: [gmx-users] Gromacs says that may GeForce 9800gt is<br />
incompatible any help?<br />
Message-ID: <D22B692A.12714%matej.repic@epfl.ch><br />
Content-Type: text/plain; charset="Windows-1252"<br />
<br />
Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series from 2010, but 9800GT is from 2008.<br />
<br />
Best,<br />
------------------------------------------------------<br />
Dr. Matej Repic<br />
Ecole Polytechnique F?d?rale de Lausanne<br />
Laboratory of Computational Chemistry and Biochemistry<br />
SB - ISIC ? LCBC<br />
BCH 4108<br />
CH - 1015 Lausanne<br />
------------------------------------------------------<br />
<br />
From: <gromacs.org_gmx-users-bounces@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces@maillist.sys.kth.se>> on behalf of Juliano Braz Carregal <julianocarregal@hotmail.com<mailto:julianocarregal@hotmail.com>><br />
Reply-To: "gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>" <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>><br />
Date: Friday, September 25, 2015 at 20:46<br />
To: "gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>" <gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>><br />
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible any help?<br />
<br />
<br />
Gromacs 5 says that may GeForce 9800gt is incompatible any help?<br />
<br />
<br />
------------------------------<br />
<br />
Message: 3<br />
Date: Fri, 25 Sep 2015 20:22:54 +0000<br />
From: Ebert Maximilian <m.ebert@umontreal.ca><br />
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br />
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters<br />
Message-ID: <5EF0A589-8604-438C-90ED-55ECB9FC21CE@umontreal.ca><br />
Content-Type: text/plain; charset="us-ascii"<br />
<br />
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?<br />
<br />
Max<br />
<br />
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul@vt.edu> wrote:<br />
> <br />
> <br />
> <br />
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:<br />
>> Hi there,<br />
>> <br />
>> I am trying to simulate a heme containing protein. I found AMBER heme<br />
>> parameters in the mol2 and frcmod file format. I know that I can generate<br />
>> .itp files containing the parameters, which I can later add to my .top file.<br />
>> However, it would be much easier to use pdb2gmx directly without stripping<br />
>> the heme and the cysteine binding the heme and later manually add it again. I<br />
>> added the cysteine to the standard amber force field. However, before adding<br />
>> the heme manually I wanted to know if there is a way to load an itp file<br />
>> while executing pdb2gmx?<br />
>> <br />
> <br />
> pdb2gmx does not need .itp information. grompp does. Add the parameters to ffbonded.itp or ffnonbonded.itp as needed.<br />
> <br />
>> How would you add the information from the cysteine in mol2 format and the<br />
>> heme in mol2/frcmod format to amber in gromacs?<br />
>> <br />
> <br />
> Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys is already supported via specbond.dat.<br />
> <br />
> -Justin<br />
> <br />
> -- <br />
> ==================================================<br />
> <br />
> Justin A. Lemkul, Ph.D.<br />
> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
> <br />
> Department of Pharmaceutical Sciences<br />
> School of Pharmacy<br />
> Health Sciences Facility II, Room 629<br />
> University of Maryland, Baltimore<br />
> 20 Penn St.<br />
> Baltimore, MD 21201<br />
> <br />
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br />
> <a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
> <br />
> ==================================================<br />
> -- <br />
> Gromacs Users mailing list<br />
> <br />
> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br />
> <br />
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> <br />
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<br />
<br />
------------------------------<br />
<br />
Message: 4<br />
Date: Fri, 25 Sep 2015 16:25:20 -0400<br />
From: Justin Lemkul <jalemkul@vt.edu><br />
To: gmx-users@gromacs.org<br />
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters<br />
Message-ID: <5605ADB0.4040608@vt.edu><br />
Content-Type: text/plain; charset=windows-1252; format=flowed<br />
<br />
<br />
<br />
On 9/25/15 4:22 PM, Ebert Maximilian wrote:<br />
> Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?<br />
><br />
<br />
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br />
<br />
-Justin<br />
<br />
> Max<br />
><br />
>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul@vt.edu> wrote:<br />
>><br />
>><br />
>><br />
>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:<br />
>>> Hi there,<br />
>>><br />
>>> I am trying to simulate a heme containing protein. I found AMBER heme<br />
>>> parameters in the mol2 and frcmod file format. I know that I can generate<br />
>>> .itp files containing the parameters, which I can later add to my .top file.<br />
>>> However, it would be much easier to use pdb2gmx directly without stripping<br />
>>> the heme and the cysteine binding the heme and later manually add it again. I<br />
>>> added the cysteine to the standard amber force field. However, before adding<br />
>>> the heme manually I wanted to know if there is a way to load an itp file<br />
>>> while executing pdb2gmx?<br />
>>><br />
>><br />
>> pdb2gmx does not need .itp information. grompp does. Add the parameters to ffbonded.itp or ffnonbonded.itp as needed.<br />
>><br />
>>> How would you add the information from the cysteine in mol2 format and the<br />
>>> heme in mol2/frcmod format to amber in gromacs?<br />
>>><br />
>><br />
>> Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys is already supported via specbond.dat.<br />
>><br />
>> -Justin<br />
>><br />
>> --<br />
>> ==================================================<br />
>><br />
>> Justin A. Lemkul, Ph.D.<br />
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
>><br />
>> Department of Pharmaceutical Sciences<br />
>> School of Pharmacy<br />
>> Health Sciences Facility II, Room 629<br />
>> University of Maryland, Baltimore<br />
>> 20 Penn St.<br />
>> Baltimore, MD 21201<br />
>><br />
>> jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br />
>> <a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
>><br />
>> ==================================================<br />
>> --<br />
>> Gromacs Users mailing list<br />
>><br />
>> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br />
>><br />
>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br />
>><br />
>> * For (un)subscribe requests visit<br />
>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a> or send a mail to gmx-users-request@gromacs.org.<br />
><br />
<br />
-- <br />
==================================================<br />
<br />
Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
<br />
Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
20 Penn St.<br />
Baltimore, MD 21201<br />
<br />
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br />
<a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
<br />
==================================================<br />
<br />
<br />
------------------------------<br />
<br />
Message: 5<br />
Date: Fri, 25 Sep 2015 20:40:19 +0000<br />
From: Ebert Maximilian <m.ebert@umontreal.ca><br />
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br />
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters<br />
Message-ID: <911260F5-AC7D-4111-BFC6-4C8C97923E44@umontreal.ca><br />
Content-Type: text/plain; charset="us-ascii"<br />
<br />
I read that and this is the way I added the cysteine to AMBER which connects to the heme. Now I am adding the heme but the FF definition for bonds, angles, etc are all in lower case for the GAFF FF. From you answer I guess I need to add these lower case atom types and the bonds, angles, etc definition from the GAFF FF to the AMBER FF manually.<br />
<br />
Not much fun but I will share the work here in the end. Maybe this will help people who want to simulate heme containing proteins in GROMACS and AMBER99SB-ILDN.<br />
<br />
Have a good weekend,<br />
Max<br />
<br />
<br />
On Sep 25, 2015, at 4:25 PM, Justin Lemkul <jalemkul@vt.edu<mailto:jalemkul@vt.edu>> wrote:<br />
<br />
<br />
<br />
On 9/25/15 4:22 PM, Ebert Maximilian wrote:<br />
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?<br />
<br />
<br />
<a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br />
<br />
-Justin<br />
<br />
Max<br />
<br />
On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul@vt.edu<mailto:jalemkul@vt.edu>> wrote:<br />
<br />
<br />
<br />
On 9/25/15 1:32 PM, Ebert Maximilian wrote:<br />
Hi there,<br />
<br />
I am trying to simulate a heme containing protein. I found AMBER heme<br />
parameters in the mol2 and frcmod file format. I know that I can generate<br />
.itp files containing the parameters, which I can later add to my .top file.<br />
However, it would be much easier to use pdb2gmx directly without stripping<br />
the heme and the cysteine binding the heme and later manually add it again. I<br />
added the cysteine to the standard amber force field. However, before adding<br />
the heme manually I wanted to know if there is a way to load an itp file<br />
while executing pdb2gmx?<br />
<br />
<br />
pdb2gmx does not need .itp information. grompp does. Add the parameters to ffbonded.itp or ffnonbonded.itp as needed.<br />
<br />
How would you add the information from the cysteine in mol2 format and the<br />
heme in mol2/frcmod format to amber in gromacs?<br />
<br />
<br />
Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys is already supported via specbond.dat.<br />
<br />
-Justin<br />
<br />
--<br />
==================================================<br />
<br />
Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
<br />
Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
20 Penn St.<br />
Baltimore, MD 21201<br />
<br />
jalemkul@outerbanks.umaryland.edu<mailto:jalemkul@outerbanks.umaryland.edu> | (410) 706-7441<br />
<a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
<br />
==================================================<br />
--<br />
Gromacs Users mailing list<br />
<br />
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br />
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<br />
<br />
--<br />
==================================================<br />
<br />
Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
<br />
Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
20 Penn St.<br />
Baltimore, MD 21201<br />
<br />
jalemkul@outerbanks.umaryland.edu<mailto:jalemkul@outerbanks.umaryland.edu> | (410) 706-7441<br />
<a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
<br />
==================================================<br />
--<br />
Gromacs Users mailing list<br />
<br />
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br />
<br />
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<br />
<br />
------------------------------<br />
<br />
Message: 6<br />
Date: Fri, 25 Sep 2015 16:43:32 -0400<br />
From: Justin Lemkul <jalemkul@vt.edu><br />
To: gmx-users@gromacs.org<br />
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters<br />
Message-ID: <5605B1F4.4050807@vt.edu><br />
Content-Type: text/plain; charset=windows-1252; format=flowed<br />
<br />
<br />
<br />
On 9/25/15 4:40 PM, Ebert Maximilian wrote:<br />
> I read that and this is the way I added the cysteine to AMBER which connects to the heme. Now I am adding the heme but the FF definition for bonds, angles, etc are all in lower case for the GAFF FF. From you answer I guess I need to add these lower case atom types and the bonds, angles, etc definition from the GAFF FF to the AMBER FF manually.<br />
><br />
<br />
Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple, but <br />
if that residue involves modifications to the force field, then there is more <br />
work to be done.<br />
<br />
-Justin<br />
<br />
> Not much fun but I will share the work here in the end. Maybe this will help people who want to simulate heme containing proteins in GROMACS and AMBER99SB-ILDN.<br />
><br />
> Have a good weekend,<br />
> Max<br />
><br />
><br />
> On Sep 25, 2015, at 4:25 PM, Justin Lemkul <jalemkul@vt.edu<mailto:jalemkul@vt.edu>> wrote:<br />
><br />
><br />
><br />
> On 9/25/15 4:22 PM, Ebert Maximilian wrote:<br />
> Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?<br />
><br />
><br />
> <a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br />
><br />
> -Justin<br />
><br />
> Max<br />
><br />
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul@vt.edu<mailto:jalemkul@vt.edu>> wrote:<br />
><br />
><br />
><br />
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:<br />
> Hi there,<br />
><br />
> I am trying to simulate a heme containing protein. I found AMBER heme<br />
> parameters in the mol2 and frcmod file format. I know that I can generate<br />
> .itp files containing the parameters, which I can later add to my .top file.<br />
> However, it would be much easier to use pdb2gmx directly without stripping<br />
> the heme and the cysteine binding the heme and later manually add it again. I<br />
> added the cysteine to the standard amber force field. However, before adding<br />
> the heme manually I wanted to know if there is a way to load an itp file<br />
> while executing pdb2gmx?<br />
><br />
><br />
> pdb2gmx does not need .itp information. grompp does. Add the parameters to ffbonded.itp or ffnonbonded.itp as needed.<br />
><br />
> How would you add the information from the cysteine in mol2 format and the<br />
> heme in mol2/frcmod format to amber in gromacs?<br />
><br />
><br />
> Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys is already supported via specbond.dat.<br />
><br />
> -Justin<br />
><br />
> --<br />
> ==================================================<br />
><br />
> Justin A. Lemkul, Ph.D.<br />
> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
><br />
> Department of Pharmaceutical Sciences<br />
> School of Pharmacy<br />
> Health Sciences Facility II, Room 629<br />
> University of Maryland, Baltimore<br />
> 20 Penn St.<br />
> Baltimore, MD 21201<br />
><br />
> jalemkul@outerbanks.umaryland.edu<mailto:jalemkul@outerbanks.umaryland.edu> | (410) 706-7441<br />
> <a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
><br />
> ==================================================<br />
> --<br />
> Gromacs Users mailing list<br />
><br />
> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List</a> before posting!<br />
><br />
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br />
><br />
> * For (un)subscribe requests visit<br />
> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a> or send a mail to gmx-users-request@gromacs.org.<br />
><br />
><br />
> --<br />
> ==================================================<br />
><br />
> Justin A. Lemkul, Ph.D.<br />
> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
><br />
> Department of Pharmaceutical Sciences<br />
> School of Pharmacy<br />
> Health Sciences Facility II, Room 629<br />
> University of Maryland, Baltimore<br />
> 20 Penn St.<br />
> Baltimore, MD 21201<br />
><br />
> jalemkul@outerbanks.umaryland.edu<mailto:jalemkul@outerbanks.umaryland.edu> | (410) 706-7441<br />
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Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
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Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
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End of gromacs.org_gmx-users Digest, Vol 137, Issue 137<br />
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