<br><br><div class="gmail_quote">On Mon, Jan 17, 2011 at 8:29 AM, <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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: Non integral charges (Erik Marklund)<br>
2. Re: Non integral charges (Justin A. Lemkul)<br>
3. Re: Viscosity calculations (Justin A. Lemkul)<br>
4. Re: Non integral charges (Kavyashree M)<br>
5. Secondary structure loss in implicit solvent simulations<br>
(K. Singhal)<br>
6. Re: Non integral charges (Vitaly Chaban)<br>
7. Re: Re: Non integral charges (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 17 Jan 2011 13:06:19 +0100<br>
From: Erik Marklund <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] Non integral charges<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:4D3430BB.20207@xray.bmc.uu.se">4D3430BB.20207@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
It's pretty close to -1. The difference stems from floating point<br>
conversion errors. There's nothing to worry about.<br>
<br>
Erik<br>
<br>
Kavyashree M skrev 2011-01-17 13.02:<br>
> Dear gromacs users,<br>
><br>
> while using grompp I got a message :<br>
><br>
> " System has non-zero total charge: -9.999998e-01"<br>
><br>
> This is non integral charges. What should I add using genion?<br>
> +1 charge? Why am I getting such non integral charges?<br>
> I also checked for any breakage in the chain and found no such<br>
> ends.<br>
><br>
> Kindly suggest<br>
><br>
> With Regards<br>
> MKS<br>
><br>
><br>
<br>
<br>
--<br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 17 Jan 2011 07:07:51 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Non integral charges<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:4D343117.2070005@vt.edu">4D343117.2070005@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Kavyashree M wrote:<br>
> Dear gromacs users,<br>
><br>
> while using grompp I got a message :<br>
><br>
> " System has non-zero total charge: -9.999998e-01"<br>
><br>
> This is non integral charges. What should I add using genion?<br>
> +1 charge? Why am I getting such non integral charges?<br>
<br>
Please see FAQ #30.<br>
<br>
<a href="http://www.gromacs.org/Documentation/FAQs" target="_blank">http://www.gromacs.org/Documentation/FAQs</a><br>
<br>
-Justin<br>
<br>
> I also checked for any breakage in the chain and found no such<br>
> ends.<br>
><br>
> Kindly suggest<br>
><br>
> With Regards<br>
> MKS<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: 3<br>
Date: Mon, 17 Jan 2011 07:11:29 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Viscosity calculations<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:4D3431F1.8070203@vt.edu">4D3431F1.8070203@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Xiaohu Li wrote:<br>
> Hi,<br>
> I'm trying to calculate viscosities of a few ionic liquid and has<br>
> roughly read about Hess's paper JCP 116 209, 2002.<br>
> Follows are the questions that I have<br>
> (1) For the method which uses the fluctuations of the pressure tensor<br>
> using Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis option<br>
> and has obtained<br>
> a few files such as evisco.xvg, eviscoi.xvg and visco.xvg<br>
> The evisco.xvg seems like the one I'm interested, since it has the title as<br>
> @ title "Shear viscosity using Einstein relation"<br>
> and the unit seems also correct. This file has 5 columns, if I<br>
> understand it correctly(by extrapolating from Hess's paper), the second<br>
> to fourth columns are the results from the off-diagonal elements of the<br>
> pressure<br>
> tensor and the fifth one being the average. Hess's paper seems to be<br>
> this one(Figure 5). However, the results are way to low for the ionic<br>
> liquid, since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid.<br>
> the eviscoi.xvg file seems to be some kind of integral of evisco.xvg<br>
> which I'm not quite getting what it is.<br>
> visco.xvg contains the shear viscosity and bulk viscosity, which again<br>
> seems to be the one I'm looking for. However, the shear viscosity I'm<br>
> looking is(the region which roughly is constant) about 3~5 times higher<br>
> than the experiment. The simulation is 12ns long. Of course, this could<br>
> mean (1) the force field is bad or (2) the Green-kudo converges too<br>
> slowly as Hess pointed out.<br>
<br>
Either of these are possible. Have you tried (1) different parameters or (2)<br>
longer simulations? If the model does not reproduce the experiment, it is not a<br>
very good model...<br></blockquote><div>What about those files evisco.xvg, eviscoi.xvg and visco.xvg? which one could be the correct file to look at?</div><div>I'm using OPLS-AA force field, the density and enthalpy of evaporation are both reasonably reproduced. However, kinetic studies using </div>
<div>OPLS-AA on ionic liquid seems scarce(or I know little enough to not aware of what has been done). </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
> Since it is not getting any useful result, I turned to non-equilibrium<br>
> MD by applying a shear external force, which is in (2)<br>
> (2) I tried both NVT and NPT simulations which uses berendsen coupling<br>
> bath. and set up the cos_acceleration = 0.1 nm/ps^2.<br>
> However, I tried to use g_energy -f *edr -s *tpr and by selecting<br>
> the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero<br>
> data points on all times.<br>
><br>
<br>
This could be related to a bug that was fixed just a few days ago. Try pulling<br>
the latest stable release from git and trying again. <br></blockquote><div>That sounds like a solution, can you provide a link?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<br>
> I tried really hard on searching results on the user list of gromacs<br>
> but it seems that there are quite a lot questions on this but not a<br>
> single satisfactory answer has been given, the most popular answer<br>
> people gave is refer to Hess's paper, but even though Hess was giving a<br>
> good theoretical background on this paper, practically on how to set up<br>
> MD jobs is not given.<br>
> So I would appreciate anyone's hint.<br>
><br>
> Cheers,<br>
><br>
> Xiaohu<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: Mon, 17 Jan 2011 17:41:51 +0530<br>
From: Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>><br>
Subject: Re: [gmx-users] Non integral charges<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<AANLkTins7nzCkP-kk0o+84f=<a href="mailto:OeD7rj2jKYfEiH9dQOmT@mail.gmail.com">OeD7rj2jKYfEiH9dQOmT@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thank you Sir!<br>
<br>
With Regards<br>
MKS<br>
<br>
On Mon, Jan 17, 2011 at 5:37 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> Kavyashree M wrote:<br>
><br>
>> Dear gromacs users,<br>
>><br>
>> while using grompp I got a message :<br>
>><br>
>> " System has non-zero total charge: -9.999998e-01"<br>
>><br>
>> This is non integral charges. What should I add using genion?<br>
>> +1 charge? Why am I getting such non integral charges?<br>
>><br>
><br>
> Please see FAQ #30.<br>
><br>
> <a href="http://www.gromacs.org/Documentation/FAQs" target="_blank">http://www.gromacs.org/Documentation/FAQs</a><br>
><br>
> -Justin<br>
><br>
><br>
> I also checked for any breakage in the chain and found no such<br>
>> ends.<br>
>><br>
>> Kindly suggest<br>
>><br>
>> With Regards<br>
>> MKS<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<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>
> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110117/3b71fe67/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110117/3b71fe67/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 17 Jan 2011 14:45:37 +0100<br>
From: "K. Singhal" <<a href="mailto:k.singhal@uva.nl">k.singhal@uva.nl</a>><br>
Subject: [gmx-users] Secondary structure loss in implicit solvent<br>
simulations<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:9C8B103A-1757-4A3E-B7E2-3A7B5E223201@uva.nl">9C8B103A-1757-4A3E-B7E2-3A7B5E223201@uva.nl</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi<br>
<br>
I have a question regarding the implicit solvent implementation in GROMACS 4.5.1 (with GPU acceleration). I have been trying to simulate molecules with varying size (PYP with 125 AAs, BBA5 with ~20 AAs, and and Trigger Factor with 432 AAs), but can't seem to be able to maintain the secondary structure in any of them. Can any one suggest a particular set of parameters than need to be taken care of or used with certain fixed values for better results?<br>
<br>
While I have used a varied range of values for almost all parameters, here is the list of parameters recently and unsuccessfully used:<br>
integrator = sd<br>
nsteps = 10000000<br>
init_step = 0<br>
ns_type = Grid<br>
nstlist = 10<br>
ndelta = 2<br>
nstcomm = 10<br>
comm_mode = Linear<br>
delta_t = 0.002<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 0<br>
epsilon_surface = 0<br>
optimize_fft = FALSE<br>
ePBC = xyz<br>
bPeriodicMols = FALSE<br>
bContinuation = FALSE<br>
bShakeSOR = FALSE<br>
etc = No<br>
nsttcouple = -1<br>
epc = No<br>
epctype = Isotropic<br>
nstpcouple = -1<br>
tau_p = 1<br>
andersen_seed = 815131<br>
rlist = 1.1<br>
rlistlong = 2.5<br>
rtpi = 0.05<br>
coulombtype = Cut-off<br>
rcoulomb_switch = 0<br>
rcoulomb = 2.5<br>
vdwtype = Cut-off<br>
rvdw_switch = 0<br>
rvdw = 2.5<br>
epsilon_r = 1<br>
epsilon_rf = 1<br>
implicit_solvent = GBSA<br>
gb_algorithm = OBC<br>
gb_epsilon_solvent = 80<br>
nstgbradii = 1<br>
rgbradii = 1.1<br>
gb_saltconc = 0.02<br>
gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br>
gb_obc_gamma = 4.85<br>
gb_dielectric_offset = 0.009<br>
sa_algorithm = Still<br>
sa_surface_tension = 2.092<br>
shake_tol = 7.5e-06<br>
bd_fric = 0.5<br>
ld_seed = 2010<br>
<br>
Thanks and Regards<br>
Kush<br>
<br>
<br>
<br>
--<br>
Kushagra Singhal<br>
Promovendus, Computational Chemistry<br>
Universiteit van Amsterdam<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 17 Jan 2011 09:25:53 -0500<br>
From: Vitaly Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><br>
Subject: [gmx-users] Re: Non integral charges<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:AANLkTimFLitXcgEhOTucxm1ERau57C9EaEMCiyiK4c%2B-@mail.gmail.com">AANLkTimFLitXcgEhOTucxm1ERau57C9EaEMCiyiK4c+-@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
> while using grompp I got a message :<br>
><br>
> " System has non-zero total charge: -9.999998e-01"<br>
><br>
> This is non integral charges. What should I add using genion?<br>
> +1 charge? Why am I getting such non integral charges?<br>
> I also checked for any breakage in the chain and found no such<br>
> ends.<br>
><br>
> Kindly suggest<br>
><br>
> With Regards<br>
> MKS<br>
<br>
Dear MKS:<br>
<br>
You should check the topology file(s) personally since it(they)<br>
presumably not healthy.<br>
<br>
--<br>
=========================<br>
Dr. Vitaly V. Chaban, Ph.D.<br>
Department of Chemistry<br>
University of Rochester<br>
Rochester, New York 14627-0216<br>
The United States of America<br>
=========================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Mon, 17 Jan 2011 09:28:44 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: Non integral charges<br>
To: <a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</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:4D34521C.6000705@vt.edu">4D34521C.6000705@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Vitaly Chaban wrote:<br>
>> while using grompp I got a message :<br>
>><br>
>> " System has non-zero total charge: -9.999998e-01"<br>
>><br>
>> This is non integral charges. What should I add using genion?<br>
>> +1 charge? Why am I getting such non integral charges?<br>
>> I also checked for any breakage in the chain and found no such<br>
>> ends.<br>
>><br>
>> Kindly suggest<br>
>><br>
>> With Regards<br>
>> MKS<br>
><br>
> Dear MKS:<br>
><br>
> You should check the topology file(s) personally since it(they)<br>
> presumably not healthy.<br>
><br>
<br>
The magnitude of the deviation from -1 (only 0.000002) is almost certainly due<br>
to rounding errors and is nothing serious in this case.<br>
<br>
-Justin<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>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 81, Issue 104<br>
******************************************<br>
</font></blockquote></div><br>