Hello Shikha<br><br>Replace NA+ with NA in your topol.top file.<br>It will solve the problem as it recognise NA for NA+.<br><br>Thanks<br><br>Yuvraj <br>IIIT Hyderabad<br><br><div class="gmail_quote">On Sun, Dec 26, 2010 at 12:26 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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<br>Today's Topics:<br>
<br>
1. Re: Replicating an experiment (David van der Spoel)<br>
2. RE: Replicating an experiment (NG HUI WEN)<br>
3. average pressure too high (sreelakshmi ramesh)<br>
4. No such moleculetype NA+ (shikha agarwal)<br>
<br><br>---------- Forwarded message ----------<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sat, 25 Dec 2010 22:55:34 +0100<br>Subject: Re: [gmx-users] Replicating an experiment<br>On 12/25/10 6:37 PM, NG HUI WEN wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein.<br>
<br>
It's good to know I can use the "generate-new-starting-velocity" method. But, do you mind to elaborate a bit more what you mean by "if you simulate long enough"?<br>
<br>
I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system,<br>
1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file<br>
2) simulate the system for a period (perhaps 1 ns)<br>
3) take any frame / final structure<br>
4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate?<br>
<br>
</blockquote>
Yes that is what I meant. Of course you should check that your protein is not unfolding, or you membrane going into the wrong phase.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks very much indeed!!<br>
<br>
________________________________<br>
<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> on behalf of David van der Spoel<br>
Sent: Sat 12/25/2010 10:28 PM<br>
To: Discussion list for GROMACS users<br>
Subject: Re: [gmx-users] Replicating an experiment<br>
<br>
<br>
<br>
On 2010-12-25 15.05, NG HUI WEN wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear all,<br>
Merry Xmas! I have a very quick question here which i'd like to pick<br>
your brain on, would really appreciate a reply.<br>
I am planning to replicate an experiment that I have carried out. Just<br>
wondering what is the best way to do it? I am thinking of changing the<br>
starting velocity of my system by setting a random number e.g 23412445<br>
etc in the gen_seed section as below, not sure if it is meaningful to do so?<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = random number<br>
Thank you for your input!<br>
</blockquote>
That will work fine, if you simulate long enough. Consider that the<br>
starting structure may also influence how different your results will<br>
be, e.g. for a protein in water. For liquids there is no such problem.<br>
You can do a simulation and slightly elevated temperature and pick<br>
structures from that with a different random seed, in order to randomize<br>
your simulations even more.<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
HW<br>
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________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
<br>
<br><br>---------- Forwarded message ----------<br>From: "NG HUI WEN" <<a href="mailto:HuiWen.Ng@nottingham.edu.my">HuiWen.Ng@nottingham.edu.my</a>><br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sun, 26 Dec 2010 09:46:05 +0800<br>Subject: RE: [gmx-users] Replicating an experiment<br><br>
Got it, thanks very much David!<br>
<br>
:)<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> on behalf of David van der Spoel<br>
Sent: Sun 12/26/2010 5:55 AM<br>
To: Discussion list for GROMACS users<br>
Subject: Re: [gmx-users] Replicating an experiment<br>
<br>
On 12/25/10 6:37 PM, NG HUI WEN wrote:<br>
> Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein.<br>
><br>
> It's good to know I can use the "generate-new-starting-velocity" method. But, do you mind to elaborate a bit more what you mean by "if you simulate long enough"?<br>
><br>
> I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system,<br>
> 1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file<br>
> 2) simulate the system for a period (perhaps 1 ns)<br>
> 3) take any frame / final structure<br>
> 4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate?<br>
><br>
Yes that is what I meant. Of course you should check that your protein<br>
is not unfolding, or you membrane going into the wrong phase.<br>
<br>
> Thanks very much indeed!!<br>
><br>
> ________________________________<br>
><br>
> From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> on behalf of David van der Spoel<br>
> Sent: Sat 12/25/2010 10:28 PM<br>
> To: Discussion list for GROMACS users<br>
> Subject: Re: [gmx-users] Replicating an experiment<br>
><br>
><br>
><br>
> On 2010-12-25 15.05, NG HUI WEN wrote:<br>
>> Dear all,<br>
>> Merry Xmas! I have a very quick question here which i'd like to pick<br>
>> your brain on, would really appreciate a reply.<br>
>> I am planning to replicate an experiment that I have carried out. Just<br>
>> wondering what is the best way to do it? I am thinking of changing the<br>
>> starting velocity of my system by setting a random number e.g 23412445<br>
>> etc in the gen_seed section as below, not sure if it is meaningful to do so?<br>
>> gen_vel = yes<br>
>> gen_temp = 300.0<br>
>> gen_seed = random number<br>
>> Thank you for your input!<br>
> That will work fine, if you simulate long enough. Consider that the<br>
> starting structure may also influence how different your results will<br>
> be, e.g. for a protein in water. For liquids there is no such problem.<br>
> You can do a simulation and slightly elevated temperature and pick<br>
> structures from that with a different random seed, in order to randomize<br>
> your simulations even more.<br>
>> HW<br>
>> <<<br>
>><br>
>> This message and any attachment are intended solely for the addressee<br>
>> and may contain confidential information. If you have received this<br>
>> message in error, please send it back to me, and immediately delete it.<br>
>> Please do not use, copy or disclose the information contained in this<br>
>> message or in any attachment. Any views or opinions expressed by the<br>
>> author of this email do not necessarily reflect the views of the<br>
>> University of Nottingham.<br>
>><br>
>> This message has been checked for viruses but the contents of an<br>
>> attachment may still contain software viruses which could damage your<br>
>> computer system: you are advised to perform your own checks. Email<br>
>> communications with the University of Nottingham may be monitored as<br>
>> permitted by UK& Malaysia legislation.<br>
>><br>
>> >><br>
>><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell& Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><<a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>><br>
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> << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.<br>
><br>
> This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK& Malaysia legislation.>><br>
><br>
<br>
<br>
--<br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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<br><br>---------- Forwarded message ----------<br>From: sreelakshmi ramesh <<a href="mailto:sree.lakshmi@research.iiit.ac.in">sree.lakshmi@research.iiit.ac.in</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Date: Sun, 26 Dec 2010 10:58:12 +0530<br>Subject: [gmx-users] average pressure too high<br>Dear users,<br> I did nvt equil and after that npt equilbriation and i am using parinello rahman as the barostat but the prob is even after 200 ps of equil the avg pressure is 1.5 bar .can anybody hepl me out with the issue.Any suggestions please.<br>
<br>sree.<br>
<br><br>---------- Forwarded message ----------<br>From: shikha agarwal <<a href="mailto:shikhaiiitabi@gmail.com">shikhaiiitabi@gmail.com</a>><br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Sun, 26 Dec 2010 12:26:16 +0530<br>Subject: [gmx-users] No such moleculetype NA+<br>hello ,<br><br>this is my ions.itp file for gromos53a6 forcefield<br><br>[ moleculetype ]<br>; molname nrexcl<br>CU1 1<br>
<br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>
1 CU1+ 1 CU1 CU 1 1 63.54600<br><br>[ moleculetype ]<br>; molname nrexcl<br>CU 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CU2+ 1 CU CU 1 2 63.54600<br>
<br>[ moleculetype ]<br>; molname nrexcl<br>ZN 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 ZN2+ 1 ZN ZN 1 2 65.37000<br>this is my ions.itp<br>
<br>[ moleculetype ]<br>; molname nrexcl<br>MG 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 MG2+ 1 MG MG 1 2 24.30500<br><br>
[ moleculetype ]<br>; molname nrexcl<br>CA 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CA2+ 1 CA CA 1 2 40.08000<br><br>[ moleculetype ]<br>
; molname nrexcl<br>NA 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 NA+ 1 NA NA 1 1 22.9898<br><br>[ moleculetype ]<br>; molname nrexcl<br>
CL 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CL- 1 CL CL 1 -1 35.45300<br><br><br><br><br>for adding ions I used this command ...<br>
<br>genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 -nname CL-<br><br>now when I m doing EM then getting this error <br><br>grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr<br>
<br>Fatal error:<br>No such moleculetype NA+<br><br><br>help me !<br><br>regards:<br>shikha<br><br>
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<br>-- <br>Yuvraj Uboveja<br>M.Tech. Bioinformatics <br>IIIT Hyderabad<br><br>