[gmx-users] Re: Eigenvalue values from PCA (a general question)
>Hi Michiel, > >I disagree, and so does semantics. The cumulative variance of a pc is the >variance of it plus the sum of the preceding ones. You're talking about the >cumulative fraction of the total variance. You are right about the proper word usage. It seemed to me from his question, the use of a % mark when discussing the variance covered by the first 10 PCs, and the conclusions drawn from the value he calculated, that Vijayan meant the cumulative fraction of the total variance. I should name it properly, but I still believe that cumulative fraction of the total variance is the property Vijayan would be interested in. Regards, Michiel > >Cheers, > >Tajerk > >On Dec 16, 2011 12:07 AM, "Niesen, Michiel" wrote: > >>Date: Thu, 15 Dec 2011 15:11:12 -0500 >>From: "R.S.K.Vijayan" >>Subject: [gmx-users] Eigenvalue values from PCA (a general question) >>To: gmx-users@gromacs.org >>Message-ID: >> >>Content-Type: text/plain; charset="iso-8859-1" > >> >Hi all > >I have a query about the eigenvalue values obtained from >g_covar and >g_anaeig > >I pe... > >>What i infer from this is that the cumulative variance experienced by the >>top 10 PC is hardly ~ ... >The cumulative variance described by a set of PCs is not the sum of their >eigenvalues. You have to take the sum of the first x eigenvalues as a >percentage of the sum of all eigenvalues to get the cumulative variance. > >>a) does this imply inadequate sampling by MD or a limited conformational >>change happening in the... > >>b) is it wise to consider the Nucleic acid during essential dynamics or >>should it be discared and ... > >>Thanking you in advance for your suggestions. My apologies since it sound >>to be a very general que... - *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Eigenvalue values from PCA (a general question)
>Date: Thu, 15 Dec 2011 15:11:12 -0500 >From: "R.S.K.Vijayan" >Subject: [gmx-users] Eigenvalue values from PCA (a general question) >To: gmx-users@gromacs.org >Message-ID: > >Content-Type: text/plain; charset="iso-8859-1" > >Hi all > >I have a query about the eigenvalue values obtained from g_covar and >g_anaeig > >I performed essential dynamics using PCA on my system (Protein-DNA >complex) considering BB of the protein and the phosphate and sugar of the >DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10 >principal components are stated below > > 1 10.1064 > 2 4.78616 > 3 4.07406 > 4 3.48535 > 5 2.7176 > 6 2.13348 > 7 1.75909 > 8 1.45699 > 9 1.12932 >10 0.893933 > >What i infer from this is that the cumulative variance experienced by the >top 10 PC is hardly ~ 30 %. The cumulative variance described by a set of PCs is not the sum of their eigenvalues. You have to take the sum of the first x eigenvalues as a percentage of the sum of all eigenvalues to get the cumulative variance. >a) does this imply inadequate sampling by MD or a limited conformational >change happening in the system >b) is it wise to consider the Nucleic acid during essential dynamics or >should it be discared and only the Protein BB or CA be considered. > >Thanking you in advance for your suggestions. My apologies since it sound >to be a very general question and rather not very specific to Gromacs. > >Regards >Vijayan.R - *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: sulfate atomtype for ffgmx (Justin A. Lemkul)
Thank you both for the suggestions. My system does also contain carbohydrates (sugar) and ffoplsaa.atp does not contain the atomtypes for these molecules. Even though carbohydrate parameters have been published for OPLS they are not present in the ffoplsaa.atp file. I did look into the available atomtypes in all the force fields in the downloaded GROMACS package (4.0.5) and the one that has most of the molecules I require is ffgmx. Perhaps the GROMOS force fields can be used as well allthough they dont have seperate sugar atomtypes (CH2 = aliphatic or sugar carbon), or the porphyrin N that is also present in my simulation. The Sulfate is also missing in GROMOS. That was the reason why I finally ended up with the decrapetated ffgmx, because it contains all but one specific atomtype I require. Should I prevent using ffgmx completely since it is decrapetated? Can the OPLS-AA carbohydrate parameters be ported to GROMACS? Or is it better to try and run my system in a different MD package that contains all specific atomtypes? Michiel _ Niesen, Michiel wrote: > > Dear all, > > I would like to perform MD simulations on a molecule that contains a > carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at > the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur > (S) and DMSO sulphur atomtypes are available. In literature I did find > GROMACS simulations performed on systems with a sulfate group but all of > them used the standard Sulfur atomtype. > If there is precedent, you may be able to use it. However, you should be warned that ffgmx is considered a deprecated force field, and in the absence of a very compelling reason to use it, probably isn't a wise choice. There are many (newer) versions of Gromos force fields that are probably more reliable. > So my question; Would it be reasonable to use the sulfur atomtype for a > sulfonyl group R-SO2-R? (as done previously in literature) If not, is > there a sulfate atomtype available for ffgmx or would you recommend me > to use another force field such as CHARMM for this system? > There are numerous sulfur atom types in OPLS-AA that may be usable. Have a look at the .atp file to see. CHARMM is not yet officially supported in Gromacs, so that force field probably isn't a viable option. -Justin > Kind regards, > Michiel _ ffgmx is deprecated, so the answer is "use another force field". In general it is not reasonable to use an atom type in a functional group that differs markedly from that it which it was parameterized. Mark _ - SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] sulfate atomtype for ffgmx
Dear all, I would like to perform MD simulations on a molecule that contains a carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur (S) and DMSO sulphur atomtypes are available. In literature I did find GROMACS simulations performed on systems with a sulfate group but all of them used the standard Sulfur atomtype. So my question; Would it be reasonable to use the sulfur atomtype for a sulfonyl group R-SO2-R? (as done previously in literature) If not, is there a sulfate atomtype available for ffgmx or would you recommend me to use another force field such as CHARMM for this system? Kind regards, Michiel - SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
