Hi Xavier,<br><br>Ok, it would be better to talk with the average values together with the corresponding error bars. For the system having smaller number of water molecules the minimum of the PMF was around -4.31+-0.97 kJ/mol, and for the other system it was around -1.75+-1.05 kJ/mol. Therefore, the difference is significant. <br>
<br>Regards<br><br><br><div class="gmail_quote">On Tue, Jun 1, 2010 at 11:30 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: number of water molecules affects the PMF (XAvier Periole)<br>
2. Re: Fatal error: Atom O in residue CO 1 not found in rtp<br>
entry with 3 atoms while sorting atoms (Nilesh Dhumal)<br>
3. Re: Fatal error: Atom O in residue CO 1 not found in rtp<br>
entry with 3 atoms while sorting atoms (Justin A. Lemkul)<br>
4. Re: Fatal error: Atom O in residue CO 1 not found in rtp<br>
entry with 3 atoms while sorting atoms (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 1 Jun 2010 21:41:42 +0200<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] number of water molecules affects the PMF<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:92B14805-6ABD-4D17-AF3D-E6C88393DD7D@rug.nl">92B14805-6ABD-4D17-AF3D-E6C88393DD7D@rug.nl</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
<br>
On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote:<br>
<br>
> Hi all,<br>
><br>
> I am trying to calculate the potential of mean force between the two<br>
> hydrophobic dipeptides (phenylalanine) in bulk water via constraint<br>
> pulling simulations. First, I calculated the mean force at each of<br>
> the constraint points, and then I integrated the mean force curve to<br>
> get the PMF.<br>
><br>
> In order to test how big the effect of the number of water molecules<br>
> on the calculated PMF I performed two sets of simulations which<br>
> differed from each other in terms of only the number of water<br>
> molecules. I used 9000 water molecules in one set, and 7000 in the<br>
> other. The overall PMF for the latter was steeper than the former,<br>
> as I expected before. However, the minimum point for the former was<br>
> around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think<br>
> that the difference should not be that much since there is not a big<br>
> difference between the number of water molecules between the two sets.<br>
Could it be that the difference is within the error ? What happens if<br>
you<br>
cut your data of each simulation in two pieces? In other words are you<br>
converged?<br>
><br>
> I searched the internet to find a study regarding the concentration<br>
> dependency of the PMF.<br>
><br>
> Is this reasonable? Any suggestions?<br>
><br>
> Regards<br>
><br>
> Ozge Engin<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
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<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 1 Jun 2010 15:42:22 -0400<br>
From: "Nilesh Dhumal" <<a href="mailto:ndhumal@andrew.cmu.edu">ndhumal@andrew.cmu.edu</a>><br>
Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found<br>
in rtp entry with 3 atoms while sorting atoms<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, "Discussion list for GROMACS users"<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:4d7dd068352ed48ab70927d368ba8ab6.squirrel@webmail.andrew.cmu.edu">4d7dd068352ed48ab70927d368ba8ab6.squirrel@webmail.andrew.cmu.edu</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
I have addes the "CO" residue.<br>
Coordinate file<br>
<br>
REMARK Accelrys Discovery Studio PDB file<br>
REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010<br>
HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C<br>
HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00 O<br>
HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00 O<br>
END<br>
<br>
in ffopla.rtp file.<br>
<br>
[ CO ] ; mandatory<br>
[ ATOMS ] ; mandatory<br>
C1 opls_974 1.00 1<br>
O2 opls_975 -0.50 2<br>
O3 opls_976 -0.50 2<br>
<br>
[ bonds ]<br>
C1 O2<br>
C1 O3<br>
<br>
I have also addes new atoms typs in ffopls.atp file.<br>
<br>
NIlesh<br>
<br>
On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:<br>
><br>
<br>
><br>
> Nilesh Dhumal wrote:<br>
><br>
>> Hello,<br>
>><br>
>><br>
>> I am getting the following error during pdb2gmx.<br>
>><br>
>><br>
>> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms<br>
>> while sorting atoms<br>
>><br>
>> I checked the pdb file and ffopls.rtp file also.<br>
>><br>
>><br>
><br>
> And what did you find? To my knowledge there is no such residue "CO" in<br>
> the ffoplsaa.rtp file. Is this something you've added? Regardless,<br>
> there's a mismatch somewhere, so if you can't identify it, post the text<br>
> of your coordinate file and the relevant .rtp entry to see if someone else<br>
> can spot it.<br>
><br>
> -Justin<br>
><br>
><br>
>> Nilesh<br>
>><br>
>><br>
>><br>
>><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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><br>
><br>
><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 01 Jun 2010 16:17:21 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found<br>
in rtp entry with 3 atoms while sorting atoms<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4C056AD1.3000804@vt.edu">4C056AD1.3000804@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
Nilesh Dhumal wrote:<br>
> I have addes the "CO" residue.<br>
> Coordinate file<br>
><br>
> REMARK Accelrys Discovery Studio PDB file<br>
> REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010<br>
> HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C<br>
> HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00 O<br>
> HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00 O<br>
> END<br>
><br>
> in ffopla.rtp file.<br>
><br>
> [ CO ] ; mandatory<br>
> [ ATOMS ] ; mandatory<br>
> C1 opls_974 1.00 1<br>
> O2 opls_975 -0.50 2<br>
> O3 opls_976 -0.50 2<br>
><br>
> [ bonds ]<br>
> C1 O2<br>
> C1 O3<br>
><br>
> I have also addes new atoms typs in ffopls.atp file.<br>
><br>
<br>
These input files work fine for me. The error message complained about an atom<br>
named "O" so be sure you're using the input you think you are. Something has<br>
gotten confused somewhere.<br>
<br>
-Justin<br>
<br>
> NIlesh<br>
><br>
> On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:<br>
><br>
>> Nilesh Dhumal wrote:<br>
>><br>
>>> Hello,<br>
>>><br>
>>><br>
>>> I am getting the following error during pdb2gmx.<br>
>>><br>
>>><br>
>>> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms<br>
>>> while sorting atoms<br>
>>><br>
>>> I checked the pdb file and ffopls.rtp file also.<br>
>>><br>
>>><br>
>> And what did you find? To my knowledge there is no such residue "CO" in<br>
>> the ffoplsaa.rtp file. Is this something you've added? Regardless,<br>
>> there's a mismatch somewhere, so if you can't identify it, post the text<br>
>> of your coordinate file and the relevant .rtp entry to see if someone else<br>
>> can spot it.<br>
>><br>
>> -Justin<br>
>><br>
>><br>
>>> Nilesh<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>> --<br>
>> ========================================<br>
>><br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>><br>
>> ========================================<br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>. Can't post? Read<br>
>> <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
>><br>
>><br>
>><br>
><br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 02 Jun 2010 06:29:45 +1000<br>
From: Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found<br>
in rtp entry with 3 atoms while sorting atoms<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:fbb49af029bfd.4c05fa59@anu.edu.au">fbb49af029bfd.4c05fa59@anu.edu.au</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Date: Wednesday, June 2, 2010 6:18<br>
Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms<br>
To: Gromacs Users' List <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
><br>
> Nilesh Dhumal wrote:<br>
> >I have addes the "CO" residue.<br>
> >Coordinate file<br>
> ><br>
> >REMARK Accelrys Discovery Studio PDB file<br>
> >REMARK Created: Fri May 28 17:26:23 Eastern<br>
> Daylight Time 2010<br>
> >HETATM 1 C1<br>
> CO 0 -<br>
> 1.044 -0.027 0.066 0.00<br>
> 0.00 C<br>
> >HETATM 2 O2<br>
> CO 0 -<br>
> 0.009 0.642 -0.037 0.00<br>
> 0.00 O<br>
> >HETATM 3 O3<br>
> CO 0 -<br>
> 2.286 0.595 -0.030 0.00<br>
> 0.00 O<br>
> >END<br>
> ><br>
> >in ffopla.rtp file.<br>
> ><br>
> >[ CO ] ; mandatory<br>
> >[ ATOMS ] ; mandatory<br>
> > C1 opls_974 1.00 1<br>
> > O2 opls_975 -0.50 2<br>
> > O3 opls_976 -0.50 2<br>
> ><br>
> >[ bonds ]<br>
> > C1 O2<br>
> > C1 O3<br>
> ><br>
> >I have also addes new atoms typs in ffopls.atp file.<br>
> ><br>
><br>
> These input files work fine for me. The error message<br>
> complained about an atom<br>
> named "O" so be sure you're using the input you think you<br>
> are. Something has<br>
> gotten confused somewhere.<br>
<br>
Perhaps the .pdb has column-formatting problems. Also, naming carbon dioxide "CO" and having two distinct atom types for its oxygen atoms, with non-neutral charge groups seems like asking for trouble...<br>
<br>
Mark<br>
<br>
><br>
> -Justin<br>
><br>
> >NIlesh<br>
> ><br>
> >On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:<br>
> ><br>
> >>Nilesh Dhumal wrote:<br>
> >><br>
> >>>Hello,<br>
> >>><br>
> >>><br>
> >>>I am getting the following error during pdb2gmx.<br>
> >>><br>
> >>><br>
> >>>Fatal error: Atom O in residue CO 1 not found in rtp entry<br>
> with 3 atoms<br>
> >>> while sorting atoms<br>
> >>><br>
> >>>I checked the pdb file and ffopls.rtp file also.<br>
> >>><br>
> >>><br>
> >>And what did you find? To my knowledge there is no such<br>
> residue "CO" in<br>
> >>the ffoplsaa.rtp file. Is this something you've<br>
> added? Regardless,<br>
> >>there's a mismatch somewhere, so if you can't identify it,<br>
> post the text<br>
> >>of your coordinate file and the relevant .rtp entry to see if<br>
> someone else<br>
> >>can spot it.<br>
> >><br>
> >>-Justin<br>
> >><br>
> >><br>
> >>>Nilesh<br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>--<br>
> >>========================================<br>
> >><br>
> >><br>
> >>Justin A. Lemkul<br>
> >>Ph.D. Candidate<br>
> >>ICTAS Doctoral Scholar<br>
> >>MILES-IGERT Trainee<br>
> >>Department of Biochemistry<br>
> >>Virginia Tech<br>
> >>Blacksburg, VA<br>
> >>jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> >><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
> >><br>
> >><br>
> >>========================================<br>
> >>--<br>
> >>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> >>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
> before posting!<br>
> >> Please don't post (un)subscribe requests to the list. Use the<br>
> >>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read<br>
> >><a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
> >><br>
> >><br>
> >><br>
> ><br>
> ><br>
> ><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ozge Engin<br> ★☆<br>